+Open data
-Basic information
Entry | Database: PDB / ID: 7t18 | ||||||
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Title | Rev1 Ternary Complex with dTTP and Ca2+ | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA Polymerase / REPLICATION / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Freudenthal, B.D. / Weaver, T.M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Authors: Weaver, T.M. / Click, T.H. / Khoang, T.H. / Todd Washington, M. / Agarwal, P.K. / Freudenthal, B.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t18.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t18.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 7t18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/7t18 ftp://data.pdbj.org/pub/pdb/validation_reports/t1/7t18 | HTTPS FTP |
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-Related structure data
Related structure data | 7t19C 7t1aC 7t1bC 5wm1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 3814.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 5052.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 51285.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: REV1, YOR346W, O6339 / Production host: Escherichia coli (E. coli) References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 4 types, 631 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-TTP / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15-23% PEG3350, 200 mM ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.66 Å / Num. obs: 60303 / % possible obs: 99.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.42 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.06 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 2977 / CC1/2: 0.529 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5WM1 Resolution: 1.7→24.66 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3548 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→24.66 Å
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Refine LS restraints |
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LS refinement shell |
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