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Yorodumi- PDB-5f9l: CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dAMPNPP A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f9l | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dAMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION | ||||||
Components |
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Keywords | Transferase/DNA / DNA polymerase / DNA enzyme / DNA damage / translesion DNA synthesis / etheno DNA adducts / Transferase-DNA complex / 1 / N2-Ethenodeoxyguanosine / Lesion bypass | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 Å | ||||||
Authors | Patra, A. / Egli, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta Authors: Patra, A. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f9l.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f9l.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9l ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9l | HTTPS FTP |
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-Related structure data
Related structure data | 5f9nC 4o3nS 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 / Fragment: UNP residues 1-432 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: 3686.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 167 molecules
#4: Chemical | ChemComp-DZ4 / | ||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % |
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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, 22% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2014 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. all: 14272 / Num. obs: 14272 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.59→2.63 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.821 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O3N Resolution: 2.592→32.442 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.9 / 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: 2.592→32.442 Å
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Refine LS restraints |
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LS refinement shell |
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