+Open data
-Basic information
Entry | Database: PDB / ID: 6x73 | ||||||
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Title | Rev1 Mg2+-facilitated Product Complex with one monophosphate | ||||||
Components |
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Keywords | REPLICATION/DNA / DNA Polymerase / REPLICATION / REPLICATION-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: 2.05 Å | ||||||
Authors | Weaver, T.M. / Freudenthal, B.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Visualizing Rev1 catalyze protein-template DNA synthesis. Authors: Weaver, T.M. / Cortez, L.M. / Khoang, T.H. / Washington, M.T. / 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 | 6x73.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x73.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 6x73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x73_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 6x73_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 6x73_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6x73_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/6x73 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x73 | HTTPS FTP |
-Related structure data
Related structure data | 6x6zC 6x70C 6x71C 6x72C 6x74C 6x75C 6x76C 6x77C 5wm1S 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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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 4103.655 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: 50320.887 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, 221 molecules
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-PO4 / |
#6: Chemical | ChemComp-NH4 / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15-23% PEG3350 and 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 PILATUS3 R 200K-A / Detector: PIXEL / Date: Oct 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→24.96 Å / Num. obs: 43725 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.95 Å2 / Rrim(I) all: 0.089 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.05→2.5662 Å / Num. unique obs: 14709 / CC1/2: 0.444 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WM1 Resolution: 2.05→24.96 Å / SU ML: 0.2411 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6294 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: 32.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→24.96 Å
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Refine LS restraints |
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LS refinement shell |
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