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Yorodumi- PDB-8gml: Crystal structure of human DNA polymerase eta incorporating 5F-dU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gml | ||||||
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Title | Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dG | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA damage / DNA replication / translesion synthesis / TRANSFERASE-DNA complex / anti-cancer / 5-FU | ||||||
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: 2.567 Å | ||||||
Authors | Jung, H. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA Authors: Jung, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gml.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gml.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gml_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8gml_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8gml_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 8gml_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gml ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gml | HTTPS FTP |
-Related structure data
Related structure data | 8gkrC 8skiC 4o3nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 3582.356 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, 50 molecules
#4: Chemical | ChemComp-B7P / |
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#5: Chemical | ChemComp-CA / |
#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: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.567→58.899 Å / Num. obs: 14525 / % possible obs: 100 % / Redundancy: 13.35 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.9931 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.567→2.614 Å / Num. unique obs: 771 / CC1/2: 0.4356 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4O3N Resolution: 2.567→49.41 Å / SU ML: 0.4273 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0988 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.567→49.41 Å
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Refine LS restraints |
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LS refinement shell |
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