+Open data
-Basic information
Entry | Database: PDB / ID: 2bsy | ||||||
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Title | Epstein Barr Virus dUTPase | ||||||
Components | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE | ||||||
Keywords | HYDROLASE / DUTPASE / MONOMER / NUCLEOTIDE METABOLISM / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information dUTP metabolic process / dUTP diphosphatase / dUTP diphosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | HUMAN HERPESVIRUS 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Tarbouriech, N. / Buisson, M. / Seigneurin, J.-M. / Cusack, S. / Burmeister, W.P. | ||||||
Citation | Journal: Structure / Year: 2005 Title: The Monomeric Dutpase from Epstein-Barr Virus Mimics Trimeric Dutpases Authors: Tarbouriech, N. / Buisson, M. / Seigneurin, J.-M. / Cusack, S. / Burmeister, W.P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bsy.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bsy.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 2bsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bsy_validation.pdf.gz | 802.6 KB | Display | wwPDB validaton report |
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Full document | 2bsy_full_validation.pdf.gz | 806.2 KB | Display | |
Data in XML | 2bsy_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2bsy_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/2bsy ftp://data.pdbj.org/pub/pdb/validation_reports/bs/2bsy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30994.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) Strain: B95-8 / Plasmid: PPROEX-HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03195, dUTP diphosphatase | ||||
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#2: Chemical | ChemComp-UMP / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | THE SIDECHAIN OF RESIDUE ARG A187 IS OBSERVED IN TWO CONFORMATIONS. A SULFATE MOEITY IS OBSERVED IN ...THE SIDECHAIN OF RESIDUE ARG A187 IS OBSERVED IN TWO CONFORMATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 8.5 / Details: 100 MM TRIS/HCL PH 8.5, 20% PEG 3350, 200 MM LISO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.07 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 38985 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.9 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→46.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.285 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.072 / 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: 14.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→46.47 Å
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Refine LS restraints |
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