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Yorodumi- PDB-4ed2: Human DNA polymerase eta - DNA ternary complex: AT crystal at pH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ed2 | ||||||
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Title | Human DNA polymerase eta - DNA ternary complex: AT crystal at pH 7.2 (Na+ HEPES) with 1 Ca2+ ion | ||||||
Components |
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Keywords | TRANSFERASE/DNA / 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 / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.711 Å | ||||||
Authors | Nakamura, T. / Zhao, Y. / Yang, W. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Watching DNA polymerase eta make a phosphodiester bond Authors: Nakamura, T. / Zhao, Y. / Yamagata, Y. / Hua, Y.J. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ed2.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ed2.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 4ed2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/4ed2 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/4ed2 | HTTPS FTP |
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-Related structure data
Related structure data | 4ecqC 4ecrC 4ecsC 4ectC 4ecuC 4ecvC 4ecwC 4ecxC 4ecyC 4eczC 4ed0C 4ed1C 4ed3C 4ed6C 4ed7C 4ed8C 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 (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: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 460 molecules
#4: Chemical | ChemComp-NA / | ||||
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#5: Chemical | ChemComp-CA / | ||||
#6: Chemical | #7: Chemical | ChemComp-DTP / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | GLU A 116 HAS THE FOLLOWING ALTERNATE CONFIGURATION. ALTERNATE A HAS GLU 116 (OCCUPANCY 0.20), ...GLU A 116 HAS THE FOLLOWING ALTERNATE CONFIGURAT |
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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: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, 6-17%(W/V) PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Jul 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→50 Å / Num. obs: 49015 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.479 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.711→26.95 Å / Occupancy max: 1.2 / Occupancy min: 0.2 / FOM work R set: 0.8832 / SU ML: 0.19 / σ(F): 0.07 / Phase error: 19.33 / 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 / Bsol: 34.955 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.13 Å2 / Biso mean: 21.4011 Å2 / Biso min: 2.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.711→26.95 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: 17
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