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Yorodumi- PDB-2xgq: Structure of yeast DNA polymerase eta in complex with C8-N-acetyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xgq | |||||||||
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Title | Structure of yeast DNA polymerase eta in complex with C8-N-acetyl-2- aminoanthracene containing DNA | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSLESION DNA SYNTHESIS / DNA-BINDING / DNA DAMAGE | |||||||||
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: 2.7 Å | |||||||||
Authors | Schneider, S. / Schorr, S. / Carell, T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta by Bulky Acetylaminofluorene DNA Adducts. Authors: Schorr, S. / Schneider, S. / Lammens, K. / 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 | 2xgq.cif.gz | 246.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xgq.ent.gz | 192.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xgq_validation.pdf.gz | 477.4 KB | Display | wwPDB validaton report |
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Full document | 2xgq_full_validation.pdf.gz | 500.3 KB | Display | |
Data in XML | 2xgq_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 2xgq_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xgq ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xgq | HTTPS FTP |
-Related structure data
Related structure data | 2xgpC 2wtfS 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
#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 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q04049, DNA-directed DNA polymerase #2: DNA chain | Mass: 2835.871 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 3489.419 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Sequence details | RESIDUES 1-513 WITH N-TERMINAL STREP-TAG | |
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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: 57.59 % / Description: NONE |
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Crystal grow | pH: 7.6 Details: 4MG/ML,11-14% PEG3350, 0.15-0.2M CACL2, 0.1M CTP, pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.919 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 44732 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WTF Resolution: 2.7→46.3 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.871 / SU B: 29.165 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OCCUPANCY OF DISORDERED ATOMS WAS SET TO ZERO AND DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.033 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→46.3 Å
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Refine LS restraints |
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