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Yorodumi- PDB-4ub3: DNA polymerase beta closed product complex with a templating cyto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ub3 | ||||||||||||
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Title | DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s | ||||||||||||
Components |
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Keywords | TRANSFERASE / LYASE/DNA / DNA polymerase / LYASE-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: 2.06 Å | ||||||||||||
Authors | Freudenthal, B.D. / Wilson, S.H. / Beard, W.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nature / Year: 2015 Title: Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Authors: Freudenthal, B.D. / Beard, W.A. / Perera, L. / Shock, D.D. / Kim, T. / Schlick, T. / 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 | 4ub3.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ub3.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 4ub3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ub3_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 4ub3_full_validation.pdf.gz | 464.5 KB | Display | |
Data in XML | 4ub3_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 4ub3_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/4ub3 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/4ub3 | HTTPS FTP |
-Related structure data
Related structure data | 4uawC 4uayC 4uazC 4ub1C 4ub2C 4ub4C 4ub5C 4ubbC 4ubcC 2fmsS C: citing same article (ref.) S: Starting model for refinement |
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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 , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4829.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3406.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 38241.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pWL11 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap56 References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 4 types, 177 molecules
#5: Chemical | #6: Chemical | ChemComp-PPV / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 27186 / % possible obs: 97.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.1 / % possible all: 91.2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FMS Resolution: 2.06→21.343 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.6 / 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: 29.715 Å2 / ksol: 0.344 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.06→21.343 Å
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Refine LS restraints |
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LS refinement shell |
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