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Yorodumi- PDB-9icy: DNA POLYMERASE BETA (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9icy | ||||||
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Title | DNA POLYMERASE BETA (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA (NON GAPPED DNA ONLY) | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR / NUCLEOTIDYLTRANSFERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information 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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / POLB-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 / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å | ||||||
Authors | Pelletier, H. / Sawaya, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 1996 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: Journal: Biochemistry / Year: 1996 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. #2: Journal: To be Published 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. #3: Journal: To be Published Title: The Role of Thumb Movement and Template Bending in Polymerase Fidelity Authors: Pelletier, H. #4: Journal: Biochemistry / Year: 1996 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: Journal: Science / Year: 1994 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: Journal: Science / Year: 1994 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9icy.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9icy.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 9icy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/9icy ftp://data.pdbj.org/pub/pdb/validation_reports/ic/9icy | HTTPS FTP |
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-Related structure data
Related structure data | 9icmC 9icwC 9icxC 9icjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 2121.436 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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06746 |
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-Non-polymers , 3 types, 128 molecules
#4: Chemical | ChemComp-SO4 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | THIS ENTRY DESCRIBES A STRUCTURE THAT IS VERY SIMILAR TO ENTRY 9ICJ. THE ONLY DIFFERENCE BETWEEN ...THIS ENTRY DESCRIBES A STRUCTURE THAT IS VERY SIMILAR TO ENTRY 9ICJ. THE ONLY DIFFERENCE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.50 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Dec 4, 1995 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 9958 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.063 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 1.4 % / Rsym value: 0.143 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 9ICJ Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
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Solvent computation | Solvent model: MOEWS / Bsol: 444.8 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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