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Yorodumi- PDB-6wk6: Crystal structure of human polymerase eta complexed with Xanthine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wk6 | ||||||
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Title | Crystal structure of human polymerase eta complexed with Xanthine containing DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DPO4 / Y-family DNA polymerase / Translesion synthesis / TRANSFERASE / extension / DNA BINDING PROTEIN-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 / regulation of DNA repair / error-prone translesion synthesis / 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 / regulation of DNA repair / error-prone translesion synthesis / 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: 2.35 Å | ||||||
Authors | Jung, H. / Lee, S. | ||||||
Citation | Journal: Biochem.J. / Year: 2020 Title: Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase. Authors: Jung, H. / Hawkins, M. / Lee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wk6.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wk6.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wk6_validation.pdf.gz | 831.3 KB | Display | wwPDB validaton report |
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Full document | 6wk6_full_validation.pdf.gz | 839.2 KB | Display | |
Data in XML | 6wk6_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6wk6_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wk6 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wk6 | HTTPS FTP |
-Related structure data
Related structure data | 6mq8C 4o3nS 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: 48325.391 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: 3583.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: DNA chain | Mass: 2506.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 63 molecules
#4: Chemical | ChemComp-0KX / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 41.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES pH 6 5 mM magnesium chloride 18% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 19116 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rpim(I) all: 0.064 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.35→2.4 Å / Num. unique obs: 1039 / CC1/2: 0.574 / Rpim(I) all: 0.431 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O3N Resolution: 2.35→49.46 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 48.18 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→49.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.47 Å
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