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Yorodumi- PDB-5wmb: Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wmb | |||||||||
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Title | Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered) | |||||||||
Components |
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Keywords | transferase/dna / benzo[a]pyrene Rev1 polymerase carcinogen lesion bypass / DNA BINDING PROTEIN / transferase-dna complex | |||||||||
Function / homology | Function and homology information deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding ...deoxycytidyl transferase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / error-free translesion synthesis / error-prone translesion synthesis / replication fork / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / chromatin / mitochondrion / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Rechkoblit, O. / Kolbanovsky, A. / Landes, H. / Geacintov, N.E. / Aggarwal, A.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2017 Title: Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase. Authors: Rechkoblit, O. / Kolbanovskiy, A. / Landes, H. / Geacintov, N.E. / Aggarwal, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wmb.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wmb.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wmb_validation.pdf.gz | 825.1 KB | Display | wwPDB validaton report |
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Full document | 5wmb_full_validation.pdf.gz | 828.8 KB | Display | |
Data in XML | 5wmb_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5wmb_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/5wmb ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wmb | HTTPS FTP |
-Related structure data
Related structure data | 5wm1C 5wm8C 2aq4S 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
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 3798.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 5037.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 49452.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: REV1, YOR346W, O6339 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 6 types, 178 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-DCP / | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PEG / | #9: 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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.25 M sodium citrate pH 6.0 buffer 15-20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→65.83 Å / Num. obs: 26824 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 18.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AQ4 Resolution: 2.25→65.83 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.251 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.837 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→65.83 Å
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