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3kd1

Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.

Method: X-RAY DIFFRACTION Dmax: 104.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase

Enterobacteria phage RB69

UniProt Q38087

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain E； UniProt 1–903 Fragment：RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase. Mutation：D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C ;DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') ; × 1 ;DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3') ; × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；5% PEG 20000, 0.1M sodium acetate pH 5, 0.1M magnesium acetate, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.66 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3KD1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B8H SLIDING CLAMP, DNA POLYMERASE Deposited 1999-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 893–903（11 aa） Fragment：RESIDUES 893-903
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.313
1CLQ CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX AT 2.7 A RESOLUTION Deposited 1999-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa） Fragment：RESIDUES 1-903
Not recorded CA CALCIUM ION × 9 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；12% (W/V) PEG 350MME, 150 MM CACL2, 100 MM SODIUM CACODYLATE, PH 6.5, 12 DEGREES C, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 2.70 Å R-free 0.284
1IG9 Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase Deposited 2001-04-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：Exonuclease-deficient (D222A/D327A) mutant CA CALCIUM ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；289 K；PEG 350 monomethyl ether, calcium chloride, sodium cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.258
1IH7 High-Resolution Structure of Apo RB69 DNA Polymerase Deposited 2001-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–903（903 aa）
Not recorded K POTASSIUM ION × 2 GMP GUANOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；285 K；Sodium citrate, sodium/potassium tartrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 2.21 Å R-free 0.258
1Q9X Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA Deposited 2003-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；PEG 350MME, Calcium chloride, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Resolution 2.69 Å R-free 0.288
1Q9X Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA Deposited 2003-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；PEG 350MME, Calcium chloride, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Resolution 2.69 Å R-free 0.288
1Q9X Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA Deposited 2003-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 3 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；PEG 350MME, Calcium chloride, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Resolution 2.69 Å R-free 0.288
1Q9X Crystal structure of Enterobacteria phage RB69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA Deposited 2003-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；PEG 350MME, Calcium chloride, Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Resolution 2.69 Å R-free 0.288
1Q9Y CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA Deposited 2003-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 350MME, Calcium chloride, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Resolution 2.80 Å R-free 0.271
1WAF DNA POLYMERASE FROM BACTERIOPHAGE RB69 Deposited 1997-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–903（903 aa）
Not recorded GMP GUANOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 3.20 Å R-free 0.274
1WAF DNA POLYMERASE FROM BACTERIOPHAGE RB69 Deposited 1997-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–903（903 aa）
Not recorded GMP GUANOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 3.20 Å R-free 0.274
1WAJ DNA POLYMERASE FROM BACTERIOPHAGE RB69 Deposited 1997-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–903（903 aa）
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.80 Å R-free 0.280
2ATQ RB69 single-stranded DNA binding protein-DNA polymerase fusion Deposited 2005-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 400, Tris-Cl, 6-aminocaproic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.345
2DTU Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog Deposited 2006-07-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–902（902 aa）
Mutation：D222A, D327A, I253G, Deletion 254-260 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES pH 7.1, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.37 Å R-free 0.268
2DTU Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog Deposited 2006-07-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–902（902 aa）
Mutation：D222A, D327A, I253G, Deletion 254-260 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES pH 7.1, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.37 Å R-free 0.268
2DTU Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog Deposited 2006-07-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–902（902 aa）
Mutation：D222A, D327A, I253G, Deletion 254-260 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES pH 7.1, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.37 Å R-free 0.268
2DTU Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog Deposited 2006-07-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–902（902 aa）
Mutation：D222A, D327A, I253G, Deletion 254-260 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES pH 7.1, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.37 Å R-free 0.268
2DY4 Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol Deposited 2006-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG2000 MME, Magnesium Sulfate, Sodium acetate, HEPES buffer pH7.0, Beta-mercaptoethanol, glycerol, 3 cycles of Macro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.65 Å R-free 0.281
2DY4 Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol Deposited 2006-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG2000 MME, Magnesium Sulfate, Sodium acetate, HEPES buffer pH7.0, Beta-mercaptoethanol, glycerol, 3 cycles of Macro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.65 Å R-free 0.281
2DY4 Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol Deposited 2006-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG2000 MME, Magnesium Sulfate, Sodium acetate, HEPES buffer pH7.0, Beta-mercaptoethanol, glycerol, 3 cycles of Macro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.65 Å R-free 0.281
2DY4 Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol Deposited 2006-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG2000 MME, Magnesium Sulfate, Sodium acetate, HEPES buffer pH7.0, Beta-mercaptoethanol, glycerol, 3 cycles of Macro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.65 Å R-free 0.281
2OYQ Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog Deposited 2007-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.86 Å R-free 0.294
2OYQ Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog Deposited 2007-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.86 Å R-free 0.294
2OYQ Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog Deposited 2007-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A MG MAGNESIUM ION × 1 N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.86 Å R-free 0.294
2OYQ Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog Deposited 2007-02-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.86 Å R-free 0.294
2OZM Crystal structure of RB69 gp43 in complex with DNA with 5-NITP opposite an abasic site analog Deposited 2007-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A MG MAGNESIUM ION × 1 N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 20000,sodium acetate, magnesium acetate, beta-mercaptoethanol, TRIS 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.86 Å R-free 0.268
2OZS Crystal structure of RB69 gp43 in complex with DNA with dATP opposite dTMP Deposited 2007-02-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A MG MAGNESIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 20000, sodium acetate, magnesium acetate, beta-mercaptoethanol, TRIS 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.75 Å R-free 0.272
2P5G Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.295
2P5G Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A,D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.295
2P5G Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A,D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.295
2P5G Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A,D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.295
2P5O Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 2–903（902 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；8% PEG 2000 MME. 100mM Magnesium sulfate, 100mM HEPES, 100mM Sodium acetate, 15% glycerol, 2mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.290
2P5O Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 2–903（902 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；8% PEG 2000 MME. 100mM Magnesium sulfate, 100mM HEPES, 100mM Sodium acetate, 15% glycerol, 2mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.290
2P5O Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 2–903（902 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；8% PEG 2000 MME. 100mM Magnesium sulfate, 100mM HEPES, 100mM Sodium acetate, 15% glycerol, 2mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.290
2P5O Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog Deposited 2007-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 2–903（902 aa）
Mutation：D222A, D327A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；8% PEG 2000 MME. 100mM Magnesium sulfate, 100mM HEPES, 100mM Sodium acetate, 15% glycerol, 2mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.290
3CFO Triple Mutant APO structure Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–903（903 aa）
Mutation：L561A/S565G/Y567A SO4 SULFATE ION × 4 GMP GUANOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.015 M MG ACETATE, 0.05M NA CACODYLATE, 1.7 M (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.235
3CFP Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 1 Deposited 2008-03-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A CA CALCIUM ION × 4 CL CHLORIDE ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；7% PEG350 monomethyl ether, 0.1M NA CACODYLATE, 0.14M CACL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.267
3CFR Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 2 Deposited 2008-03-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A CA CALCIUM ION × 5 CL CHLORIDE ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；7% PEG350 monomethyl ether, 0.1M NA CACODYLATE, 0.1 M CA2CL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.266
3CQ8 Ternary complex of the L415F mutant RB69 exo(-)polymerase Deposited 2008-04-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa） Fragment：RB69 polymerase
Mutation：L415F, D222A, D327A CA CALCIUM ION × 6 NA SODIUM ION × 3 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；220mM CaCl2, 25% monometheyl ether PEG350, and 50mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.50 Å R-free 0.281
3KD5 Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid. Deposited 2009-10-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain E 1–903（903 aa） Fragment：RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase.
Mutation：D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C PPF PHOSPHONOFORMIC ACID × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；5% PEG 20000, 0.1M sodium acetate pH5, 0.1M magnesium acetate, 0.1M Tris HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.69 Å R-free 0.263
3L8B Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin Deposited 2009-12-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；reservoir: 12% PEG2000MME, 100mM Sodium Acetate, 150mM Magnesium Sulfate, 100mM Hepes pH 7.0, 6% Glycerol and 2mM Beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.15 Å R-free 0.255
3L8B Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin Deposited 2009-12-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；reservoir: 12% PEG2000MME, 100mM Sodium Acetate, 150mM Magnesium Sulfate, 100mM Hepes pH 7.0, 6% Glycerol and 2mM Beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.15 Å R-free 0.255
3LDS Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG Deposited 2010-01-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, I563S DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；3% PEG 20000, 100mM sodium acetate, 100mM manganese acetate, 100mM Tris-HCl, 1% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 3.00 Å R-free 0.295
3LZI RB69 DNA Polymerase (Y567A) ternary complex with dATP Opposite 7,8-dihydro-8-oxoguanine Deposited 2010-03-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions micro-batch vapor-diffusion；pH 6.5；293.15 K；150 mM CaCl2, 11%(w/v) PEG 350 monomethyl ether MME, and 100 mM Na Cacodylate pH 6.5 , micro-batch vapor-diffusion, temperature 293.15K
Resolution 2.30 Å R-free 0.258
3LZJ RB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,8-Dihydro-8-oxoguanine Deposited 2010-03-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, Y567A CTP CYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions micro-batch vapor-diffusion；pH 6.5；293.15 K；150 mM CaCl2, 14%(w/v) PEG 350 monomethyl ether (MME), and 100 mM Na Cacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293.15K
Resolution 2.05 Å R-free 0.251
3NAE RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin Deposited 2010-06-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions micro-batch vapor-diffusion；pH 6.5；293 K；15%(w/v) PEG 350 monomethyl ether (MME), 150 mM CaCl2, and 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Resolution 2.00 Å R-free 0.231
3NCI RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution Deposited 2010-06-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa） Fragment：DNA polymerase
Mutation：D222A, D327A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions micro-batch vapor-diffusion；pH 6.5；293 K；8%(w/v) PEG 350 monomethyl ether (MME),160 mM CaCl2, and 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Resolution 1.79 Å R-free 0.201
3NDK RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG Deposited 2010-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions micro-batch vapor-diffusion；pH 6.5；293 K；10% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Resolution 2.00 Å R-free 0.229
3NE6 RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG Deposited 2010-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, S565G, Y567A CA CALCIUM ION × 5 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；293 K；7% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Resolution 2.00 Å R-free 0.226
3NGI RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG Deposited 2010-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions micro-batch vapor-diffusion；pH 6.5；293 K；13%(w/v) PEG 350 monomethyl ether (MME), 150 mM CaCl2, 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K
Resolution 1.89 Å R-free 0.226
3NHG RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dTTP Opposite dG Deposited 2010-06-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；293 K；apply 7% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, and 100 mM NaCacodylate (pH 6.5) to crystal Y567A/S565G: P/T:dCTP ternary complex and then soak dTTP into the crystal to replace dCTP in the ternary complex, micro-batch vapor-diffusion, temperature 293K
Resolution 2.50 Å R-free 0.244
3QEI RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite Difluorotoluene Nucleoside Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 2.18 Å R-free 0.238
3QEP RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite Difluorotoluene Nucleoside Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 1.80 Å R-free 0.204
3QER RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dATP Opposite Difluorotoluene Nucleoside Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 1.96 Å R-free 0.217
3QES RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite Difluorotoluene Nucleoside Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 1.98 Å R-free 0.218
3QET RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite dT Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 2.08 Å R-free 0.217
3QEV RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dT Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 1.77 Å R-free 0.210
3QEW RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dDTP Opposite dT Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.84 Å R-free 0.205
3QEX RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite dT Deposited 2011-01-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 1.73 Å R-free 0.206
3QNN RB69 DNA Polymerase (Y567A) Ternary Complex with dGT Opposite 3tCo Deposited 2011-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15%(w/v) PEG350 monomethyl ether (MME), and 100mM sodium cacodylate (pH6.5), VAPOR DIFFUSION, temperature 298K
Resolution 1.92 Å R-free 0.214
3QNO RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite 3tCo Deposited 2011-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；150 mM CaCl2, 15%(w/v) PEG350 monomethyl ether (MME), and 100mM sodium cacodylate (pH6.5), VAPOR DIFFUSION, temperature 298K
Resolution 1.88 Å R-free 0.212
3RMA Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；10-11 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes, 6-10 % glycerol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 7.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.84 Å R-free 0.275
3RMA Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；10-11 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes, 6-10 % glycerol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 7.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.84 Å R-free 0.275
3RMA Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；10-11 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes, 6-10 % glycerol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 7.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.84 Å R-free 0.275
3RMA Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；10-11 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes, 6-10 % glycerol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 7.2, VAPOR DIFFUSION, HANGING DROP
Resolution 2.84 Å R-free 0.275
3RMB Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；6.5 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes pH 7.2, 6% glycerol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K
Resolution 2.65 Å R-free 0.276
3RMB Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；6.5 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes pH 7.2, 6% glycerol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K
Resolution 2.65 Å R-free 0.276
3RMB Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；6.5 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes pH 7.2, 6% glycerol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K
Resolution 2.65 Å R-free 0.276
3RMB Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；6.5 % PEG 2000 MME, 100 mM Na acetate, 150 mM MgSO4, 100 mM Hepes pH 7.2, 6% glycerol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K
Resolution 2.65 Å R-free 0.276
3RMC Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4.5 % PEG 20,000, 150 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.282
3RMC Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4.5 % PEG 20,000, 150 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.282
3RMC Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4.5 % PEG 20,000, 150 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.282
3RMC Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4.5 % PEG 20,000, 150 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.282
3RMD Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4% PEG 20,000, 100 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 2.98 Å R-free 0.275
3RMD Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4% PEG 20,000, 100 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 2.98 Å R-free 0.275
3RMD Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4% PEG 20,000, 100 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 2.98 Å R-free 0.275
3RMD Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol Deposited 2011-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；4% PEG 20,000, 100 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol, 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP
Resolution 2.98 Å R-free 0.275
3RWU RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Difluorotoluene Nucleoside Deposited 2011-05-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% (w/v) PEG350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH6.5), VAPOR DIFFUSION, temperature 298K
Resolution 2.33 Å R-free 0.276
3S9H RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+ Deposited 2011-06-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L561A,S565G,Y567A CA CALCIUM ION × 7 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH VAPOR DIFFUSION；pH 6.5；293.15 K；150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Resolution 1.95 Å R-free 0.213
3SCX RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+ Deposited 2011-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L561A,S565G,Y567A DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH VAPOR DIFFUSION；pH 6.5；293.15 K；150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Resolution 2.35 Å R-free 0.259
3SI6 RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mg2+ Deposited 2011-06-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G,Y567A DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH VAPOR DIFFUSION；pH 6.5；293.15 K；150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Resolution 1.85 Å R-free 0.217
3SJJ RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+ Deposited 2011-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G,Y567A DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH VAPOR DIFFUSION；pH 6.5；293.15 K；150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Resolution 2.38 Å R-free 0.265
3SNN RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dG in the presence of Mg2+ Deposited 2011-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH VAPOR DIFFUSION；pH 6.5；293.15 K；150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, soak crystals with the same buffer containing 100 mM magnesium chloride instead of calcium chloride, MICROBATCH VAPOR DIFFUSION, temperature 293.15K
Resolution 2.00 Å R-free 0.222
3SPY RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA Deposited 2011-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：L415A, L561A, S565G, Y567A UPC 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine × 1 MG MAGNESIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.14 Å R-free 0.242
3SPZ DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+) Deposited 2011-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L415A, L561A, S565G, Y567A UPC 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.43 Å R-free 0.257
3SQ0 DNA Polymerase(L561A/S565G/Y567A) Ternary Complex with dUpNpp Opposite dA (Mn2+) Deposited 2011-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.00 Å R-free 0.245
3SQ1 RB69 DNA Polymerase Ternary Complex with dUpCpp Opposite dA Deposited 2011-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：yes DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.82 Å R-free 0.213
3SQ2 RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence) Deposited 2011-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–902（902 aa）
Mutation：yes TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.10 Å R-free 0.244
3SQ4 RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC rich sequence) Deposited 2011-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–902（902 aa）
Mutation：yes TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.23 Å R-free 0.238
3SUN RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (AT rich sequence) Deposited 2011-07-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–895（895 aa）
Mutation：Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.42 Å R-free 0.255
3SUO RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (GC rich sequence) Deposited 2011-07-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–900（900 aa）
Mutation：Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.23 Å R-free 0.255
3SUP RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (GC rich sequence) Deposited 2011-07-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.32 Å R-free 0.261
3SUQ RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (AT rich sequence) Deposited 2011-07-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–897（897 aa）
Mutation：Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 3.15 Å R-free 0.300
3TAB 5-hydroxycytosine paired with dGMP in RB69 gp43 Deposited 2011-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% PEG 2000-MME, 100 mM NaOAc, 100 mM MgSO4, 100 mM Hepes, 5% glycerol, 1 mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.80 Å R-free 0.281
3TAB 5-hydroxycytosine paired with dGMP in RB69 gp43 Deposited 2011-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% PEG 2000-MME, 100 mM NaOAc, 100 mM MgSO4, 100 mM Hepes, 5% glycerol, 1 mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.80 Å R-free 0.281
3TAB 5-hydroxycytosine paired with dGMP in RB69 gp43 Deposited 2011-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% PEG 2000-MME, 100 mM NaOAc, 100 mM MgSO4, 100 mM Hepes, 5% glycerol, 1 mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.80 Å R-free 0.281
3TAB 5-hydroxycytosine paired with dGMP in RB69 gp43 Deposited 2011-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% PEG 2000-MME, 100 mM NaOAc, 100 mM MgSO4, 100 mM Hepes, 5% glycerol, 1 mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.80 Å R-free 0.281
3TAE 5-hydroxycytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.71 Å R-free 0.268
3TAE 5-hydroxycytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.71 Å R-free 0.268
3TAE 5-hydroxycytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.71 Å R-free 0.268
3TAE 5-hydroxycytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.71 Å R-free 0.268
3TAF 5-fluorocytosine paired with ddGMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.00 Å R-free 0.280
3TAF 5-fluorocytosine paired with ddGMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.00 Å R-free 0.280
3TAF 5-fluorocytosine paired with ddGMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.00 Å R-free 0.280
3TAF 5-fluorocytosine paired with ddGMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.00 Å R-free 0.280
3TAG 5-fluorocytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.284
3TAG 5-fluorocytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.284
3TAG 5-fluorocytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.284
3TAG 5-fluorocytosine paired with dAMP in RB69 gp43 Deposited 2011-08-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 1–903（903 aa）
Mutation：D222A, D327A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7% Peg 2000-MME, 100mM NaOAc, 100mM MgSO4, 100mM Hepes, 5% glycerol, 1mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.284
3UIQ RB69 DNA Polymerase Ternary Complex containing dUpNpp Deposited 2011-11-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150mM CaCl2, 15% PEG 350 MME, 100mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.88 Å R-free 0.220
4DTJ RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddT/dA as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.202
4DTM RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.95 Å R-free 0.220
4DTN RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.96 Å R-free 0.216
4DTO RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Not recorded DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.05 Å R-free 0.225
4DTP RB69 DNA Polymerase Ternary Complex with dGTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Not recorded DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.05 Å R-free 0.229
4DTR RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.04 Å R-free 0.228
4DTS RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, L565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.96 Å R-free 0.206
4DTU RB69 DNA Polymerase Ternary Complex with dGTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.86 Å R-free 0.201
4DTX RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.84 Å R-free 0.206
4DU1 RB69 DNA Polymerase Ternary Complex with dATP Opposite dT Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.15 Å R-free 0.245
4DU3 RB69 DNA Polymerase Ternary Complex with dDTP Opposite dT with 3-Deaza-adenine at the N-1 Position of Template Strand Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.02 Å R-free 0.227
4DU4 RB69 DNA Polymerase Ternary Complex with dATP Opposite dT with 3-Deaza-adenine at the N-3 Position of Primer Strand Deposited 2012-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.28 Å R-free 0.249
4E3S RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT Deposited 2012-03-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：L561A, S565G, Y567A QTP 3-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7-methyl-3H-imidazo[4,5-b]pyridine × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150mM CaCl2, 15% PEG350 MME, 100mM sodium cacodylate (pH6.5), VAPOR DIFFUSION, temperature 298K
Resolution 2.04 Å R-free 0.219
4FJ5 RB69 DNA polymerase ternary complex with dATP/dT Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.05 Å R-free 0.238
4FJ7 RB69 DNA polymerase ternary complex with dGTP/dT Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.213
4FJ8 RB69 DNA polymerase ternary complex with dCTP/dT Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.19 Å R-free 0.252
4FJ9 RB69 DNA polymerase ternary complex with dTTP/dT Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), 100 mM sodium cacodylate pH 6.5 , VAPOR DIFFUSION, temperature 298K
Resolution 1.97 Å R-free 0.235
4FJG RB69 DNA polymerase ternary complex with dATP/dC Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5 , VAPOR DIFFUSION, temperature 298K
Resolution 2.02 Å R-free 0.264
4FJH RB69 DNA polymerase ternary complex with dGTP/dC Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.11 Å R-free 0.223
4FJI RB69 DNA polymerase ternary complex with dcTP/dC Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5 , VAPOR DIFFUSION, temperature 298K
Resolution 2.20 Å R-free 0.264
4FJJ RB69 DNA polymerase ternary complex with dTTP/dC Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5 , VAPOR DIFFUSION, temperature 298K
Resolution 1.99 Å R-free 0.225
4FJK RB69 DNA polymerase ternary complex with dATP/dA Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.00 Å R-free 0.226
4FJL RB69 DNA polymerase ternary complex with dGTP/dA Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.87 Å R-free 0.223
4FJM RB69 DNA polymerase ternary complex with dCTP/dA Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.02 Å R-free 0.232
4FJN RB69 DNA polymerase ternary complex with dTTP/dA Deposited 2012-06-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5 , VAPOR DIFFUSION, temperature 298K
Resolution 1.98 Å R-free 0.240
4FJX RB69 DNA polymerase ternary complex with dATP/dG Deposited 2012-06-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5 , VAPOR DIFFUSION, temperature 298K
Resolution 2.11 Å R-free 0.225
4FK0 RB69 DNA polymerase ternary complex with dCTP/dG Deposited 2012-06-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 2.18 Å R-free 0.252
4FK2 RB69 DNA polymerase ternary complex with dTTP/dG Deposited 2012-06-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.98 Å R-free 0.225
4FK4 RB69 DNA polymerase ternary complex with dGTP/dG Deposited 2012-06-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, L415A, L561A, S565G, Y567A DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.222
4I9L Crystal structure of the D714A mutant of RB69 DNA polymerase Deposited 2012-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, D714A GMP GUANOSINE × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；1.65 M AMMONIUM SULPHATE, 0.01 M MAGNESIUM CHLORIDE, 0.05 M SODIUM CITRATE DIHYDROGEN, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 2.60 Å R-free 0.249
4I9Q Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase Deposited 2012-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A D327A,Y567A,D714A XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 2 CA CALCIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；10% PEG 8000, 0.2 M (NH4)2SO4 and 0.1 M sodium citrate (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.287
4I9Q Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase Deposited 2012-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A D327A,Y567A,D714A XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 2 CA CALCIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；10% PEG 8000, 0.2 M (NH4)2SO4 and 0.1 M sodium citrate (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.287
4J2A RB69 DNA Polymerase L415A Ternary Complex Deposited 2013-02-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：L415A, D222A, D327A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% PEG350 monomethyl ether (MME), and 100 mM Sodium Carcodylate , pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.80 Å R-free 0.211
4J2B RB69 DNA Polymerase L415G Ternary Complex Deposited 2013-02-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa） Fragment：RB69 DNA polymerase
Mutation：L415G, D222A, D327A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% PEG350 monomethyl ether (MME), and 100 mM Sodium Carcodylate (pH6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 2.04 Å R-free 0.220
4J2D RB69 DNA Polymerase L415K Ternary Complex Deposited 2013-02-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa）
Mutation：L415K, D222A, D327A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% PEG350 monomethyl ether (MME), and 100 mM Sodium Cacodylate , pH 6.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.76 Å R-free 0.197
4J2E RB69 DNA Polymerase L415M Ternary Complex Deposited 2013-02-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–901（901 aa） Fragment：RB69 DNA polymerase
Mutation：L415M, D222A, D327A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 15% PEG350 monomethyl ether (MME), and 100 mM Sodium Carcodylate (pH6.5), VAPOR DIFFUSION, temperature 298K
Resolution 2.02 Å R-free 0.213
4KHN Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase Deposited 2013-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A, D327A, Y567A, D714A XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；12% PEG 8000, 0.1 M MES, 0.2 Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6
Resolution 2.55 Å R-free 0.211
4KHN Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase Deposited 2013-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–903（903 aa）
Mutation：D222A, D327A, Y567A, D714A XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 2 CA CALCIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；12% PEG 8000, 0.1 M MES, 0.2 Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6
Resolution 2.55 Å R-free 0.211
4KHQ Ternary complex of RB69 mutant L415F wit DUMPNPP Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D327A, D222A, L415F CA CALCIUM ION × 3 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；50 MM TRIS, PH 7.5, 10% PEG350, 180 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, temperature 298K
Resolution 2.19 Å R-free 0.212
4KHS Ternary complex of RB69 mutant L415F with a ribonucleotide at 0 position Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D327A, D222A, L415F CA CALCIUM ION × 3 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；50 MM TRIS-HCL, 10% PEG350, 220 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, pH 7.5, temperature 298K
Resolution 2.12 Å R-free 0.216
4KHU Ternary complex of rb69 mutant L415F with a ribonucleotide at -1 position Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D327A, D222A, L415F TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；50 MM TRIS-HCL, 13% PEG350, 180 MM CALCIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.05 Å R-free 0.247
4KHW Ternary complex of RB69 mutant L415F with ribonucleotide at -2 position Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D327A, D222A, L415F TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 8 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；50 MM TRIS-HCL, 19% PEG350, 180 MM CALCIUM CHLORIDE,, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.37 Å R-free 0.224
4KHY Ternary complex of rb69 mutant L415F with ribonucleotide at -3 position Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：YES TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 NA SODIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；298 K；50 MM TRIS-HCL, 17.5% PEG350, 180 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, temperature 298K
Resolution 2.25 Å R-free 0.241
4KI4 Ternary complex of rb69 mutant L415F with ribonucleotides at 0 and -1 position Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D327A, D222A, L415F TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 4 NA SODIUM ION × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；50 MM TRIS-HCL, 16% PEG350, 180 MM CALCIUM CHLORIDE , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.45 Å R-free 0.221
4KI6 Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position Deposited 2013-05-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D327A, D222A, L415F TTP THYMIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；50 MM TRIS-HCL, 16% PEG350, 180 MM CALCIUM CHLORIDE, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.55 Å R-free 0.233
4M3R RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, temperature 298K
Resolution 2.07 Å R-free 0.221
4M3T RB69 DNA polymerase ternary complex with dT/dG at position n-2 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 1.90 Å R-free 0.209
4M3U RB69 DNA polymerase ternary complex with dT/dG at position n-3 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 2.07 Å R-free 0.223
4M3W RB69 DNA polymerase ternary complex with dT/dG at position n-4 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 2.10 Å R-free 0.220
4M3X RB69 DNA polymerase ternary complex with dT/dG at position n-5 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 2.20 Å R-free 0.241
4M3Y RB69 DNA polymerase ternary complex with dG/dT at position n-1 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 1.86 Å R-free 0.221
4M3Z RB69 DNA polymerase ternary complex with dG/dT at position n-2 of primer/tempLate duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 1.84 Å R-free 0.207
4M41 RB69 DNA polymerase ternary complex with dG/dT at position n-3 of primer/tempLate duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 2.15 Å R-free 0.237
4M42 RB69 DNA polymerase ternary complex with dG/dT at position n-4 of primer/tempLate duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 2.04 Å R-free 0.224
4M45 RB69 DNA polymerase ternary complex with dG/dT at position n-5 of primer/template duplex Deposited 2013-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–903（903 aa）
Mutation：D222A,D327A,L415A,L561A,S565G,Y567A ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
Resolution 1.89 Å R-free 0.214
7F4Y Crystal structure of replisomal dimer of DNA polymerase from bacteriophage RB69 with DNA duplexes Deposited 2021-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 1–903（903 aa）
Chain B 1–903（903 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；sodium acetate, isopropanol, magnesium chloride, sodium chloride, spermine tetrahydrochloride
Resolution 2.20 Å R-free 0.245

120 other PDB entries and 166 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOL_BPR69
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–903； UniProt 1–903

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3kd1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3kd1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3kd1
Deposition date deposition_date2009-10-22
Structure title titleClosed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.
Keywords keywords;gp43, polymerase, HCMV, human cytomegalovirus, acyclovir, acyclic guanosine, foscavir, foscarnet, phosphonoformic acid, DNA replication, DNA-binding, DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, TRANSFERASE-DNA COMPLEX ;; TRANSFERASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.02 Å
Radius of gyration Rg (electron density) rg_electron31.05 Å
Forward intensity I(0) i0221747000.00
Molecular weight molecular_weight114400.0 kDa
Excluded volume excluded_volume141160 ų
Envelope volume envelope_volume184980 ų
Hydration-shell volume shell_volume47820 ų
Envelope diameter envelope_diameter109.7 Å
Shell Rg shell_rg39.54 Å
Envelope Rg envelope_rg31.09 Å
Shape Rg shape_rg31.05 Å
Total Rg total_rg31.75 Å
Total atoms total_atoms8028
Residues n_residues936
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.1 Å
Rg (real space) rg_real31.79 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real2.2170e+08
I(0) uncertainty (real space) i0_real_error3.1690e+06
Rg (reciprocal space) rg_reciprocal31.89 Å
I(0) (reciprocal space) i0_reciprocal221800000.0000
Solution quality estimate total_estimate0.8897
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.5 Å
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40060000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3kd1E01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology342 — DNA Polymerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — DNA Polymerase, chain B, domain 1
Domain ID domain_id3kd1E02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3kd1E03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id3kd1E04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
Domain ID domain_id3kd1E05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily300 —
Domain ID domain_id3kd1E06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1820 — Ribonuclease H-like motif
Homologous superfamily homologous superfamily10 — DnaQ-like 3'-5' exonuclease
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8. Citations (1)

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9. Files and Curves (10)