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Yorodumi- PDB-5dlg: Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dlg | ||||||
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Title | Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine | ||||||
Components |
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Keywords | Transferase/DNA / Catalytic Domain / DNA Damage / DNA-Directed DNA Polymerase / Guanosine Triphosphate / Y-family polymerase / trans-lesion synthesis (TLS) / DNA Binding / O4-Alkylthymidine / O4-Methylthymidine / Transferase-DNA complex | ||||||
Function / homology | Function and homology information response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / 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 / error-free translesion synthesis / DNA synthesis involved in DNA repair / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å | ||||||
Authors | Patra, A. / OFlaherty, D.K. / Egli, M. | ||||||
Citation | Journal: Chem Sci / Year: 2016 Title: Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta. Authors: O'Flaherty, D.K. / Patra, A. / Su, Y. / Guengerich, F.P. / Egli, M. / Wilds, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dlg.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dlg.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 5dlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dlg_validation.pdf.gz | 799.4 KB | Display | wwPDB validaton report |
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Full document | 5dlg_full_validation.pdf.gz | 804.8 KB | Display | |
Data in XML | 5dlg_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 5dlg_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlg ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlg | HTTPS FTP |
-Related structure data
Related structure data | 5dlfC 5dqgC 5dqhC 5dqiC 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 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 PT
#2: DNA chain | Mass: 2426.617 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: 3651.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 226 molecules
#4: Chemical | ChemComp-GOL / | ||||
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#5: Chemical | #6: Chemical | ChemComp-XG4 / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.69 % |
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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, 20% 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: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 18606 / Num. obs: 18606 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 10.457 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 0.941 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O3N Resolution: 2.351→37.899 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.46 / 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: 2.351→37.899 Å
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Refine LS restraints |
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LS refinement shell |
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