+Open data
-Basic information
Entry | Database: PDB / ID: 2okb | ||||||
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Title | High Resolution Crystal Structures of Vaccinia Virus dUTPase | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / Fold / jelly-roll / Superfamily / dUTPase-like / forms tight trimer through an additional beta-sheet in each subunit / subunit beta-sheets are orthogonally packed around the three-fold axis | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Schormann, N. / Chattopadhyay, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structures of vaccinia virus dUTPase and its nucleotide complexes. Authors: Samal, A. / Schormann, N. / Cook, W.J. / Delucas, L.J. / Chattopadhyay, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2okb.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2okb.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 2okb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2okb_validation.pdf.gz | 474.1 KB | Display | wwPDB validaton report |
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Full document | 2okb_full_validation.pdf.gz | 479.4 KB | Display | |
Data in XML | 2okb_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2okb_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/2okb ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2okb | HTTPS FTP |
-Related structure data
Related structure data | 2okdC 2okeC 2ol0C 2ol1C 1q5uS 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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Details | The asymmetric unit contains a homo-trimer with monomers related by non-crystallographic symmetry. This homo-trimer constitutes the biological assembly. |
-Components
#1: Protein | Mass: 15141.015 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Gene: DUT / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: GenBank: 29692147, UniProt: A4GD96*PLUS, dUTP diphosphatase #2: Chemical | #3: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 298 K / pH: 4.2 Details: 12% PEG1000, 0.1M lithium sulfate, 0.1M phosphate/citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 2005 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→49.7 Å / Num. obs: 20238 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 6 / Rsym value: 0.144 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q5U Resolution: 2.15→18.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.681 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.221 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→18.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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