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Open data
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Basic information
Entry | Database: PDB / ID: 6x77 | ||||||
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Title | Rev1 R518A Ternary Complex with dCTP and Ca2+ | ||||||
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![]() | REPLICATION/DNA / DNA polymerase / REPLICATION / REPLICATION-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Weaver, T.M. / Freudenthal, B.D. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.7 KB | Display | ![]() |
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PDB format | ![]() | 162.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.5 KB | Display | ![]() |
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Full document | ![]() | 797.7 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x6zC ![]() 6x70C ![]() 6x71C ![]() 6x72C ![]() 6x73C ![]() 6x74C ![]() 6x75C ![]() 6x76C ![]() 5wm1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 4748.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 50234.773 Da / Num. of mol.: 1 / Mutation: R518A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: REV1, YOR346W, O6339 / Production host: ![]() ![]() References: UniProt: P12689, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 3 types, 445 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-DCP / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.15 % |
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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: ![]() |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jul 22, 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: 1.64→25 Å / Num. obs: 49631 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.56 Å2 / Rrim(I) all: 0.128 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.64→1.9324 Å / Num. unique obs: 8792 / CC1/2: 0.616 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5WM1 Resolution: 1.64→24.89 Å / SU ML: 0.1601 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6944 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: 20.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→24.89 Å
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Refine LS restraints |
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LS refinement shell |
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