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Yorodumi- PDB-4r65: Ternary complex crystal structure of R258A mutant of DNA polymera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r65 | ||||||
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Title | Ternary complex crystal structure of R258A mutant of DNA polymerase Beta | ||||||
Components |
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Keywords | Transferase/DNA / DNA Polymerase Beta / Conformational Change / enzyme mechanism / 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 / 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 | Homo sapiens (human) Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Batra, V.K. / Beard, W.A. / Wilson, S.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Substrate-induced DNA Polymerase beta Activation. Authors: Beard, W.A. / Shock, D.D. / Batra, V.K. / Prasad, R. / Wilson, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r65.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r65.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 4r65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r65_validation.pdf.gz | 784.4 KB | Display | wwPDB validaton report |
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Full document | 4r65_full_validation.pdf.gz | 786.5 KB | Display | |
Data in XML | 4r65_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 4r65_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r65 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r65 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38155.555 Da / Num. of mol.: 1 / Mutation: R258A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pWL-11 / Production host: Escherichia coli (E. coli) References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 4853.158 Da / Num. of mol.: 1 / Fragment: Template Strand / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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#3: DNA chain | Mass: 3061.004 Da / Num. of mol.: 1 / Fragment: Primer Strand / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Fragment: Downstream Primer Strand / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
-Non-polymers , 5 types, 404 molecules
#5: Chemical | ChemComp-DUP / | ||||||
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#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CL / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 16-18% PEG3350, 50 mM Imidazole, 350 mM Sodium Acetate, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5408 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 26, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Viramax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5408 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 28340 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.075 / Χ2: 1.048 / Net I/σ(I): 17.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20.736 Å / FOM work R set: 0.8544 / SU ML: 0.28 / σ(F): 0.03 / Phase error: 22.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.704 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.55 Å2 / Biso mean: 25.62 Å2 / Biso min: 10.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20.736 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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