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Yorodumi- PDB-2wtf: DNA polymerase eta in complex with the cis-diammineplatinum (II) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wtf | ||||||
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Title | DNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3- GTG intrastrand cross-link | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / NUCLEOTIDYLTRANSFERASE / TRANSLESION DNA SYNTHESIS / TRANSFERASE / DNA-BINDING / DNA SYNTHESIS / DNA REPLICATION / MUTATOR PROTEIN / DNA DAMAGE / DNA REPAIR | ||||||
Function / homology | Function and homology information 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 ...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 / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Reissner, T. / Schneider, S. / Ziv, O. / Schorr, S. / Livneh, Z. / Carell, T. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 Title: Crystal Structure of a Cisplatin-(1,3-Gtg) Cross-Link within DNA Polymerase Eta. Authors: Reissner, T. / Schneider, S. / Schorr, S. / Carell, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wtf.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wtf.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wtf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/2wtf ftp://data.pdbj.org/pub/pdb/validation_reports/wt/2wtf | HTTPS FTP |
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-Related structure data
Related structure data | 1jihS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8092, -0.2888, 0.5116), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60708.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-513 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PDEST007 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q04049, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 4 molecules OSPT
#2: DNA chain | Mass: 5089.297 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CISPLATIN 1,3 GTG INTRASTRAND CROSS-LINK BETWEEN O 3 AND O 5, S 3 AND S 5 #3: DNA chain | Mass: 2811.846 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 134 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: 3.04 Å3/Da / Density % sol: 48 % Description: MR PHASES WERE COMBINED WITH PLATINUM SAD PHASES USING SHARP |
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Crystal grow | Details: 4MG/ML, 11-14% PEG3350, 0.15-0.2M CACL2, 0.1M ATP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0766 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0766 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.68 Å / Num. obs: 55019 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JIH Resolution: 2.5→48 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.913 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A 510-513 DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.906 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48 Å
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