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Yorodumi- PDB-4o3r: Crystal structure of human polymerase eta extending an 8-oxog dna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o3r | ||||||
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Title | Crystal structure of human polymerase eta extending an 8-oxog dna lesion: post insertion of 8-oxog-da pair | ||||||
Components |
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Keywords | Transferase/DNA / Catalytic Domain / DNA / DNA Damage / DNA-Directed DNA Polymerase / Cytosine Triphosphate / Y-family polymerase / trans-lesion synthesis (TLS) / DNA Binding / 8-oxoG lesion bypass / Transferase-DNA complex | ||||||
Function / homology | Function and homology information response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Patra, A. / Egli, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta Authors: Patra, A. / Nagy, L.D. / Zhang, Q. / Su, Y. / Muller, L. / Guengerich, F.P. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o3r.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o3r.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o3r_validation.pdf.gz | 836.8 KB | Display | wwPDB validaton report |
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Full document | 4o3r_full_validation.pdf.gz | 843.1 KB | Display | |
Data in XML | 4o3r_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 4o3r_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o3r ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o3r | HTTPS FTP |
-Related structure data
Related structure data | 4o3nC 4o3oC 4o3pC 4o3qC 4o3sC 4ecqS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y253, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3694.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized |
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#3: DNA chain | Mass: 2435.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized |
-Non-polymers , 4 types, 537 molecules
#4: Chemical | ChemComp-0KX / | ||||
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#5: Chemical | #6: Chemical | #7: 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: 2.1 Å3/Da / Density % sol: 41.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M MES pH 5.5, 5mM magnesium chloride, 16.5% PEG 2000 MME , VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→50 Å / Num. obs: 57390 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 25.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ECQ Resolution: 1.62→42.701 Å / SU ML: 0.16 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 19.9 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→42.701 Å
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Refine LS restraints |
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LS refinement shell |
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