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- PDB-9icw: DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9icw | ||||||
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Title | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; NATIVE STRUCTURE | ||||||
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![]() | TRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR / NUCLEOTIDYLTRANSFERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA / TRANSFERASE-DNA complex | ||||||
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 / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...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 / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pelletier, H. / Sawaya, M.R. | ||||||
![]() | ![]() 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. #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: 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. #4: ![]() Title: Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis Authors: Pelletier, H. / Sawaya, M.R. #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 | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 69.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9icmC ![]() 9icxC ![]() 9icyC ![]() 1bpbS ![]() 2bpgS 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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1 |
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 2088.397 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 1833.242 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 , 3 types, 160 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 59.3 % |
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Crystal grow | pH: 6.5 Details: SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE., pH 6.50 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Sep 12, 1991 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 15291 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.202 / % possible all: 81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BPB, 2BPG Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
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Solvent computation | Solvent model: MOEWS / Bsol: 427.9 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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