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Yorodumi- PDB-5l1i: Crystal Structure of Human DNA Polymerase Eta Inserting dCTP Oppo... -
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-Basic information
Entry | Database: PDB / ID: 5l1i | ||||||||||||
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Title | Crystal Structure of Human DNA Polymerase Eta Inserting dCTP Opposite O6-Methyl-2'-deoxyguanosine | ||||||||||||
Components |
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Keywords | Transferase/DNA / Catalytic Domain / DNA Damage / DNA Polymerase / Lesion bypass / O6-Methyl-2'-deoxyguanosine / Y-family polymerase / translesion DNA synthesis (TLS) / DNA Binding protein. / 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 / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) SYNTHETIC CONSTRUCT (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||||||||
Authors | Patra, A. / Egli, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta. Authors: Patra, A. / Zhang, Q. / Guengerich, F.P. / Egli, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l1i.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l1i.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 5l1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l1i_validation.pdf.gz | 782.3 KB | Display | wwPDB validaton report |
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Full document | 5l1i_full_validation.pdf.gz | 785.3 KB | Display | |
Data in XML | 5l1i_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 5l1i_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/5l1i ftp://data.pdbj.org/pub/pdb/validation_reports/l1/5l1i | HTTPS FTP |
-Related structure data
Related structure data | 5l1jC 5l1kC 5l1lC 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 TP
#2: DNA chain | Mass: 3676.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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#3: DNA chain | Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 143 molecules
#4: Chemical | ChemComp-DCP / | ||||
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#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 Calcium chloride, 15% 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: Jun 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→50 Å / Num. obs: 11577 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.169 / Rsym value: 0.169 / Net I/σ(I): 10.647 |
Reflection shell | Resolution: 2.78→2.84 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 1.579 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O3N Resolution: 2.78→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.908 / SU B: 15.955 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.131 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→50 Å
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