+Open data
-Basic information
Entry | Database: PDB / ID: 2we1 | ||||||
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Title | EBV dUTPase mutant Asp131Asn with bound dUMP | ||||||
Components | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE | ||||||
Keywords | HYDROLASE / PYROPHOSPHATASE / EPSTEIN-BARR VIRUS / NUCLEOTIDE METABOLISM / DUTPASE / MONOMER / HERPES VIRUS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Freeman, L. / Buisson, M. / Tarbouriech, N. / Burmeister, W.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: The Flexible Motif V of Epstein-Barr Virus Deoxyuridine 5'-Triphosphate Pyrophosphatase is Essential for Catalysis. Authors: Freeman, L. / Buisson, M. / Tarbouriech, N. / Van Der Heyden, A. / Labbe, P. / Burmeister, W.P. #1: 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 | 2we1.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2we1.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 2we1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/2we1 ftp://data.pdbj.org/pub/pdb/validation_reports/we/2we1 | HTTPS FTP |
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-Related structure data
Related structure data | 2we0C 2we2C 2we3C 2bsyS 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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Unit cell |
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-Components
#1: Protein | Mass: 31664.328 Da / Num. of mol.: 1 / Mutation: YES 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 / References: UniProt: P03195, dUTP diphosphatase | ||||
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#2: Chemical | ChemComp-UMP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.3 M AMMONIUM SULFATE, 25 % PEG 3350, 0.1 M HEPES PH 7, 10 MM DUTP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 10, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→46.57 Å / Num. obs: 24052 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.56 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.16 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BSY Resolution: 1.8→46.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.081 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.142 / 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: 17.495 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.57 Å
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Refine LS restraints |
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