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Open data
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Basic information
Entry | Database: PDB / ID: 2we1 | ||||||
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Title | EBV dUTPase mutant Asp131Asn with bound dUMP | ||||||
![]() | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE | ||||||
![]() | HYDROLASE / PYROPHOSPHATASE / EPSTEIN-BARR VIRUS / NUCLEOTIDE METABOLISM / DUTPASE / MONOMER / HERPES VIRUS | ||||||
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 | ![]() | 71.2 KB | Display | ![]() |
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PDB format | ![]() | 50 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.4 KB | Display | ![]() |
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Full document | ![]() | 802.6 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2we0C ![]() 2we2C ![]() 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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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.) ![]() Strain: B95-8 / Plasmid: PPROEX HTB / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-UMP / | ||||
#3: Chemical | #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: 39.6 % / 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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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