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- PDB-9ica: 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: 9ica | ||||||
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Title | DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-O-(1-THIOTRIPHOSPHATE), SOAKED IN THE PRESENCE OF DATP(ALPHA)S AND MNCL2 | ||||||
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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 / salivary gland morphogenesis / 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 ...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 / salivary gland morphogenesis / 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 / 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: 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 | ![]() | 91 KB | Display | ![]() |
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PDB format | ![]() | 70.3 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 ![]() 9icbC ![]() 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 , 3 types, 138 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/STP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/STP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-STP / | #6: 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(ALPHA)S, 1 MILLIMOLAR MNCL2, 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 13, 1995 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 9260 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 5.7 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 1.6 % / Rsym value: 16 / % possible all: 79 |
Reflection | *PLUS Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 79 % / Rmerge(I) obs: 0.16 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 8ICB Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
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Solvent computation | Solvent model: MOEWS / Bsol: 607.1 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→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: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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