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Yorodumi- PDB-4oda: Crystal structure of the vaccinia virus DNA polymerase holoenzyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oda | ||||||
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Title | Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminus | ||||||
Components |
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Keywords | HYDROLASE/REPLICATION / DNA polymerase processivity factor / DNA / DNA polymerase E9 / HYDROLASE-REPLICATION complex | ||||||
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: 2.2 Å | ||||||
Authors | Contesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Burmeister, W.P. / Iseni, F. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit d4 in complex with the a20 N-terminal domain. Authors: Contesto-Richefeu, C. / Tarbouriech, N. / Brazzolotto, X. / Betzi, S. / Morelli, X. / Burmeister, W.P. / Iseni, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oda.cif.gz | 234.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oda.ent.gz | 189.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4oda ftp://data.pdbj.org/pub/pdb/validation_reports/od/4oda | HTTPS FTP |
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-Related structure data
Related structure data | 4od8SC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26729.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Strain: Copenhagen / Gene: D4R, UNG / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P20536, uracil-DNA glycosylase #2: Protein | Mass: 5807.586 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-50 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Strain: Copenhagen / Gene: A20R / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P20995 #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.79 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 100 mM bicine, 1.5 M ammonium sulfate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2012 / Details: Si111 monochromator and toroidal mirror |
Radiation | Monochromator: Si 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9394 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→54.02 Å / Num. all: 37537 / Num. obs: 37537 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OD8 Resolution: 2.2→44.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.489 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.682 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→44.29 Å
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Refine LS restraints |
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