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Yorodumi- PDB-2r8j: Structure of the Eukaryotic DNA Polymerase eta in complex with 1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r8j | ||||||
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Title | Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin containing DNA | ||||||
Components |
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Keywords | REPLICATION / TRANSFERASE/DNA / protein-cisplatin-DNA-dNTP complex / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication ...Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Carell, T. / Alt, A. / Lammens, K. | ||||||
Citation | Journal: Science / Year: 2007 Title: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta Authors: Alt, A. / Lammens, K. / Chiocchini, C. / Lammens, A. / Pieck, J.C. / Kuch, D. / Hopfner, K.P. / Carell, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r8j.cif.gz | 244 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r8j.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r8j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2r8j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2r8j_validation.xml.gz | 44 KB | Display | |
Data in CIF | 2r8j_validation.cif.gz | 59.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/2r8j ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r8j | HTTPS FTP |
-Related structure data
Related structure data | 2r8kC 1jihS 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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2 |
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Unit cell |
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-Components
-DNA chain , 2 types, 4 molecules QPUT
#1: DNA chain | Mass: 2835.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYN #2: DNA chain | Mass: 3294.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYN |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 62617.781 Da / Num. of mol.: 2 / Fragment: Catalytic domain Source method: isolated from a genetically manipulated source Details: MAN Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YPH499 (ATCC 76625) / Gene: RAD30, DBH1 / Plasmid: pExp007 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 Rosetta / References: UniProt: Q04049, DNA-directed DNA polymerase |
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-Non-polymers , 4 types, 129 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.89 Å3/Da / Density % sol: 57.39 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 170 mM Calcium chloride, 16% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 30191 / Num. obs: 30191 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 40.053 Å2 / Rsym value: 0.154 / Net I/σ(I): 16.98 |
Reflection shell | Highest resolution: 3.1 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 5.71 / Rsym value: 0.443 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JIH Resolution: 3.1→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.1 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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