+Open data
-Basic information
Entry | Database: PDB / ID: 5jks | |||||||||
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Title | vaccinia virus D4 R167A mutant /A20(1-50) | |||||||||
Components |
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Keywords | HYDROLASE/REPLICATION / DNA POLYMERASE PROCESSIVITY FACTOR / DNA BINDING / DNA POLYMERASE BINDING / HYDROLASE-REPLICATION COMPLEX / hydrolase | |||||||||
Function / homology | Function and homology information uracil-DNA glycosylase / viral DNA genome replication / uracil DNA N-glycosylase activity / DNA replication / DNA repair / DNA binding Similarity search - Function | |||||||||
Biological species | Vaccinia virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | |||||||||
Authors | Contesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Burmeister, W.P. / Peyrefitte, C.N. / Iseni, F. | |||||||||
Funding support | France, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Structural analysis of point mutations at the Vaccinia virus A20/D4 interface. Authors: Contesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Burmeister, W.P. / Peyrefitte, C.N. / Iseni, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jks.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jks.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/5jks ftp://data.pdbj.org/pub/pdb/validation_reports/jk/5jks | HTTPS FTP |
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-Related structure data
Related structure data | 5jkrC 5jktC 4odaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26643.371 Da / Num. of mol.: 2 / Mutation: R167A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: UNG, D4R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20536, uracil-DNA glycosylase #2: Protein | Mass: 5807.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FRAGMENT: N-TERMINAL RESIDUES 1-50 / Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: A20R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20995 #3: Chemical | ChemComp-SO4 / #4: 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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1M bicine pH 7.8, 1.6M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 107 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→28.84 Å / Num. obs: 18696 / % possible obs: 99.6 % / Redundancy: 9.7 % / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.79→2.95 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.5 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ODA Resolution: 2.79→28.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.655 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 2.261 / ESU R Free: 0.33 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.262 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→28.84 Å
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Refine LS restraints |
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