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Yorodumi- PDB-4j9m: Human DNA polymerase eta-DNA ternary complex: misincorporation G ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j9m | ||||||
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Title | Human DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after an A at the primer 3' end (AA/G) | ||||||
Components |
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Keywords | TRANSFERASE/DNA / immunoglobulin / A to G transition / misincorporation / wobble base pair / DNA polymerase / 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: 2.25 Å | ||||||
Authors | Zhao, Y. / Gregory, M. / Biertumpfel, C. / Hua, Y. / Hanaoka, F. / Yang, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta. Authors: Zhao, Y. / Gregory, M.T. / Biertumpfel, C. / Hua, Y.J. / Hanaoka, F. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j9m.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j9m.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 4j9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j9m_validation.pdf.gz | 783 KB | Display | wwPDB validaton report |
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Full document | 4j9m_full_validation.pdf.gz | 790.5 KB | Display | |
Data in XML | 4j9m_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4j9m_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/4j9m ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9m | HTTPS FTP |
-Related structure data
Related structure data | 4j9kC 4j9lC 4j9nC 4j9oC 4j9pC 4j9qC 4j9rC 4j9sC 3mr2S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: catalytic core domain, UNP residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS / References: UniProt: Q9Y253, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3652.402 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 2714.811 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 194 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-XG4 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG2K-MME, KCl, MES, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 5, 2010 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→30 Å / Num. all: 21507 / Num. obs: 21434 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 25.76 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.5 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MR2 Resolution: 2.25→29.55 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8504 / SU ML: 0.27 / σ(F): 1.35 / σ(I): 0 / Phase error: 22.33 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.11 Å2 / Biso mean: 24.477 Å2 / Biso min: 6.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→29.55 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: 12
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