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- PDB-9icb: DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9icb | ||||||
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Title | DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND COCL2 | ||||||
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![]() | TRANSFERASE/DNA / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pelletier, H. / Sawaya, M.R. | ||||||
![]() | ![]() Title: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Authors: Pelletier, H. / Sawaya, M.R. #1: ![]() Title: Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates Authors: Sawaya, M.R. / Rawson, T. / Wilson, S.H. / Kraut, J. / Pelletier, H. #2: ![]() Title: The Role of Thumb Movement and Template Bending in Polymerase Fidelity Authors: Pelletier, H. #3: ![]() Title: Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #4: ![]() Title: A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #6: ![]() Title: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP Authors: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. #7: ![]() Title: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism Authors: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1nomC ![]() 1zqaC ![]() 1zqbC ![]() 1zqcC ![]() 1zqdC ![]() 1zqeC ![]() 1zqfC ![]() 1zqgC ![]() 1zqhC ![]() 1zqiC ![]() 1zqjC ![]() 1zqkC ![]() 1zqlC ![]() 1zqmC ![]() 1zqnC ![]() 1zqoC ![]() 1zqpC ![]() 1zqqC ![]() 1zqrC ![]() 1zqsC ![]() 1zquC ![]() 1zqvC ![]() 1zqwC ![]() 1zqxC ![]() 1zqyC ![]() 1zqzC ![]() 8icaC ![]() 8icbSC ![]() 8iccC ![]() 8iceC ![]() 8icfC ![]() 8icgC ![]() 8ichC ![]() 8iciC ![]() 8iczC ![]() 9icaC ![]() 9iccC ![]() 9iceC ![]() 9icgC ![]() 9ichC ![]() 9iciC ![]() 9icjC ![]() 9iclC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2112.422 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 38241.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 143 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DTP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-DTP / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | A POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE ...A POSSIBLE PHYSIOLOGI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.4 % | ||||||||||||||||||||||||
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Crystal grow![]() | pH: 6.5 Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE ...Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR COCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE. | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 298 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 8, 1995 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 8214 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 5.9 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 1.4 % / Rsym value: 12.9 / % possible all: 89 |
Reflection | *PLUS Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 89 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure![]() Starting model: 8ICB Resolution: 3.2→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
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Solvent computation | Solvent model: MOEWS / Bsol: 880.4 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.151 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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