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Open data
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Basic information
Entry | Database: PDB / ID: 2we2 | ||||||
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Title | EBV dUTPase double mutant Gly78Asp-Asp131Ser with dUMP | ||||||
![]() | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE | ||||||
![]() | HYDROLASE / DUTPASE / MONOMER / HERPES VIRUS / EPSTEIN-BARR VIRUS / NUCLEOTIDE METABOLISM | ||||||
Function / homology | ![]() dUTP metabolic process / dUTP diphosphatase / dUTP diphosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Freeman, L. / Buisson, M. / Tarbouriech, N. / Burmeister, W.P. | ||||||
![]() | ![]() 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: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.7 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.7 KB | Display | ![]() |
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Full document | ![]() | 807.3 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2we0C ![]() 2we1C ![]() 2we3C ![]() 2bsyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31695.340 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: B95-8 / Plasmid: PPROEX HTB / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-UMP / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.9 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.3 M AMMONIUM SULFATE, PEG 3350 25%, 0.1 M HEPES PH 7, AND 10 MM DUTP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→56.98 Å / Num. obs: 41744 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.38 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.89 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.51 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BSY Resolution: 1.5→45.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.624 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.085 / 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: 17.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→45.93 Å
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Refine LS restraints |
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