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1dk3

REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA

Method: SOLUTION NMR Dmax: 59.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA POLYMERASE BETA

Rattus norvegicus

UniProt P06766

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–87 Fragment：N-TERMINAL DOMAIN, RESIDUES 1-87 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.7；300 K；Ionic strength (raw mmCIF value) 400；Pressure AMBIENT NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition：2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS- D11; 400MM NACL NMR sample composition：2 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11; 100MM NACL NMR sample composition：4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11; 400MM NACL NMR sample composition：2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS- D11; 400MM NACL NMR sample composition：1.4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87); 5MM TRIS-D11; 400MM NACL Resolution not provided

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 1DK3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BNO NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA, MINIMIZED AVERAGE STRUCTURE Deposited 1996-04-25 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–86（86 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1 - 87
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；300 K
Resolution not provided
1BNP NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA, 55 STRUCTURES Deposited 1996-04-25 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–86（86 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1 - 87
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；300 K
Resolution not provided
1BPB CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM Deposited 1994-04-12 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1BPD CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM Deposited 1994-04-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.60 Å
1BPE CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON POLYMERASE MECHANISM Deposited 1994-04-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
1DK2 REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA Deposited 1999-12-06 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–86（86 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-87
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 400 mM NACL；Pressure AMBIENT
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100 mM NACL；Pressure AMBIENT
NMR sample composition 2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS- D11; 400MM NACL
NMR sample composition 2 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11; 100MM NACL
NMR sample composition 4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11; 400MM NACL
NMR sample composition 2.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS- D11; 400MM NACL
NMR sample composition 1.4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87); 5MM TRIS-D11; 400MM NACL
Resolution not provided
1HUO CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP Deposited 2001-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–335（335 aa）
Not recorded CR CHROMIUM ION × 1 TTE PHOSPHOMETHYL PHOSPHONIC ACID DEOXYTHYMIDYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；8% PEG 3350, 70mM lithium sulfate, 100mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.288
1HUO CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP Deposited 2001-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–335（335 aa）
Not recorded CR CHROMIUM ION × 1 TTE PHOSPHOMETHYL PHOSPHONIC ACID DEOXYTHYMIDYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；8% PEG 3350, 70mM lithium sulfate, 100mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.288
1HUZ CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP Deposited 2001-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–335（335 aa）
Not recorded CR CHROMIUM ION × 1 MDN METHYLENEDIPHOSPHONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；8% PEG3350, 70mM lithium sulfate, 100mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.286
1HUZ CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP Deposited 2001-01-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–335（335 aa）
Not recorded CR CHROMIUM ION × 1 MDN METHYLENEDIPHOSPHONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；8% PEG3350, 70mM lithium sulfate, 100mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.60 Å R-free 0.286
1JN3 FIDELITY PROPERTIES AND STRUCTURE OF M282L MUTATOR MUTANT OF DNA POLYMERASE: SUBTLE STRUCTURAL CHANGES INFLUENCE THE MECHANISM OF NUCLEOTIDE DISCRIMINATION Deposited 2001-07-22 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 84–334（251 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 85 - 335
Mutation：M282L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；16% PEG 3350, 5mM ammonium sulfate, 150mM sodium acetate, 50mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.35 Å R-free 0.256
1NOM DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR) Deposited 1996-04-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 1 MONTH: PEG 1500, 15% HEPES, 75 MILLIMOLAR, PH 7.5 NACL, 50 MILLIMOLAR DTT, 0.1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.5
Resolution 3.00 Å
1RPL 2.3 ANGSTROMS CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DNA POLYMERASE BETA Deposited 1994-10-25 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 84–334（251 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1ZQU DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR Deposited 1996-04-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Resolution 2.60 Å
1ZQV DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF CACL2 (150 MILLIMOLAR) Deposited 1996-04-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CACL2, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Resolution 2.70 Å
1ZQW DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF CSCL (150 MILLIMOLAR) Deposited 1996-04-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CSCL, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Resolution 2.30 Å
1ZQX DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR) Deposited 1996-04-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% TRIS-HCL, 100 MILLIMOLAR, PH 7.5 KCL, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Resolution 2.50 Å
1ZQY DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MGCL2 (50 MILLIMOLAR) Deposited 1996-04-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% TRIS-HCL, 100 MILLIMOLAR, PH 7.5 MGCL2, 50 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Resolution 2.30 Å
1ZQZ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (50 MILLIMOLAR) Deposited 1996-04-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa） Fragment：C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% TRIS-HCL, 100 MILLIMOLAR, PH 7.5 MNCL2, 50 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Resolution 2.70 Å
2BPC CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM Deposited 1994-07-08 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–334（248 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
2BPF STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP Deposited 1994-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–334（334 aa）
Not recorded MG MAGNESIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 2.90 Å
2BPG STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP Deposited 1994-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–334（334 aa）
Not recorded MG MAGNESIUM ION × 1 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 3.60 Å
2BPG STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP Deposited 1994-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–334（334 aa）
Not recorded DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.50
Resolution 3.60 Å
2VAN Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses Deposited 2007-09-03 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 90–334（245 aa） Fragment：31K DOMAIN, RESIDUES 90-334
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.249
3K75 X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain Deposited 2009-10-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 91–335（245 aa） Fragment：UNP residues 91 to 335
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.295
3K75 X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain Deposited 2009-10-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 91–335（245 aa） Fragment：UNP residues 91 to 335
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M Tri-potassium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.295
3LQC X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain Deposited 2010-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 142–335（194 aa）
Not recorded NA SODIUM ION × 1 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% PEG 3350, 0.2-0.3M TRI-POTASSIUM CITRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.250
3UXN Crystal Structure of Rat DNA Polymerase Beta, Wild Type Apoenzyme Deposited 2011-12-05 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–335（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；PEG 3350, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.50 Å R-free 0.317
3UXN Crystal Structure of Rat DNA Polymerase Beta, Wild Type Apoenzyme Deposited 2011-12-05 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–335（335 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；PEG 3350, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.50 Å R-free 0.317
3UXO Crystal Structure of Rat DNA Polymerase Beta Mutator I260Q Apoenzyme Deposited 2011-12-05 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–335（335 aa）
Mutation：I260Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；PEG 3350, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.10 Å R-free 0.318
3UXO Crystal Structure of Rat DNA Polymerase Beta Mutator I260Q Apoenzyme Deposited 2011-12-05 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–335（335 aa）
Mutation：I260Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；PEG 3350, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.10 Å R-free 0.318
3UXP Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP Deposited 2011-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–335（335 aa）
Mutation：I260Q D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；Peg3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.72 Å R-free 0.292
3UXP Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP Deposited 2011-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 1–335（335 aa）
Mutation：I260Q D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；Peg3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.72 Å R-free 0.292
3V72 Crystal Structure of Rat DNA polymerase beta Mutator E295K: Enzyme-dsDNA Deposited 2011-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–335（335 aa）
Mutation：E295K NA SODIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；296 K；PEG 3350, NaCl, Glycerol, Cacodylate, pH 6.5, vapor diffusion, temperature 296K
Resolution 2.49 Å R-free 0.291
3V7J Co-crystal structure of Wild Type Rat polymerase beta: Enzyme-DNA binary complex Deposited 2011-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 4–335（332 aa）
Not recorded NA SODIUM ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；PEG 3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.25 Å R-free 0.243
3V7K Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex Deposited 2011-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 4–335（332 aa）
Mutation：K72E NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；PEG 3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.27 Å R-free 0.277
3V7L Apo Structure of Rat DNA polymerase beta K72E variant Deposited 2011-12-21 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–335（332 aa）
Mutation：K72E NA SODIUM ION × 2 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；PEG 3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.66 Å R-free 0.335

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View Construct and Data Evidence
UniProt name DPOB_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–87； UniProt 1–87

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

SAXS scattering curve SAXS Profile

SAXS profile for 1dk3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dk3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dk3
Deposition date deposition_date1999-12-06
Structure title titleREFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA
Keywords keywords;DNA-BINDING, DEOXYRIBOSE 5'-PHOSPHATE LYASE, NUCLEOTIDYLTRANSFERASE, TRANSFERASE ;; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.46 Å
Radius of gyration Rg (electron density) rg_electron14.28 Å
Forward intensity I(0) i01917450.00
Molecular weight molecular_weight9604.0 kDa
Excluded volume excluded_volume12248 ų
Envelope volume envelope_volume15877 ų
Hydration-shell volume shell_volume10084 ų
Envelope diameter envelope_diameter56.7 Å
Shell Rg shell_rg19.04 Å
Envelope Rg envelope_rg14.82 Å
Shape Rg shape_rg14.20 Å
Total Rg total_rg15.70 Å
Total atoms total_atoms1397
Residues n_residues87
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax59.5 Å
Rg (real space) rg_real15.43 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real1.9170e+06
I(0) uncertainty (real space) i0_real_error2.5320e+04
Rg (reciprocal space) rg_reciprocal15.43 Å
I(0) (reciprocal space) i0_reciprocal1917000.0000
Solution quality estimate total_estimate0.8134
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.8 Å
Skewness Skewness skewness0.252
Kurtosis Kurtosis kurtosis-0.213
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha248000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.582; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1dk3a_
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family familya.60.6.1 — DNA polymerase beta, N-terminal domain-like

CATH v4.4 (1 domains)

Domain ID domain_id1dk3A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily110 — DNA polymerase beta, N-terminal domain-like
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8. Citations (3)

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9. Files and Curves (10)