+Open data
-Basic information
Entry | Database: PDB / ID: 3osp | ||||||
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Title | Structure of rev1 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA Polymerase / damage bypass / DNA / abasic site / nucleus / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nair, D.T. / Aggarwal, A.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase. Authors: Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / 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 | 3osp.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3osp.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 3osp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/3osp ftp://data.pdbj.org/pub/pdb/validation_reports/os/3osp | HTTPS FTP |
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-Related structure data
Related structure data | 2aq4S 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: 49452.965 Da / Num. of mol.: 1 / Fragment: Rev1 (UNP RESIDUES 305-738 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: O6339, REV1, YOR346W / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 4918.191 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3502.308 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 154 molecules
#4: Chemical | ChemComp-DCP / | ||
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#5: Chemical | #6: 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: 4.34 Å3/Da / Density % sol: 71.65 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2005 |
Radiation | Monochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 35470 / Num. obs: 33331 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AQ4 Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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LS refinement shell | Resolution: 2.5→2.52 Å /
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