DNA polymerase
Enterobacteria phage RB69
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 A； UniProt 1–903 | Mutation：D222A, D327A | ;DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*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*TP*CP*AP*A)-3') ; × 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 |
| 2 | Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts | Chain B； UniProt 1–903 | Mutation：D222A, D327A | ;DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*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*TP*CP*AP*A)-3') ; × 1 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 |
| 3 | Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts | Chain C； UniProt 1–903 | Mutation：D222A, D327A | ;DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*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*TP*CP*AP*A)-3') ; × 1 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 |
| 4 | Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts | Chain D； UniProt 1–903 | Mutation：D222A, D327A | ;DNA (5'-D(*CP*GP*TP*(CTG)P*G*AP*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*TP*CP*AP*A)-3') ; × 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 |
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 3RMD | 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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 | 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 |
| 3KD1 Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair. Deposited 2009-10-22 | 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 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 | 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 |
| 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 |
| 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 163 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | DPOL_BPR69 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–903； UniProt 1–903 Author chain B； PDBConstruct 1–903； UniProt 1–903 Author chain C； PDBConstruct 1–903； UniProt 1–903 Author chain D； PDBConstruct 1–903； UniProt 1–903 |
