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- PDB-2we1: EBV dUTPase mutant Asp131Asn with bound dUMP -

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Basic information

Entry
Database: PDB / ID: 2we1
TitleEBV dUTPase mutant Asp131Asn with bound dUMP
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
KeywordsHYDROLASE / 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
Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFreeman, 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
DepositionMar 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2615
Polymers31,6641
Non-polymers5964
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.624, 56.859, 81.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / DUTPASE / DUTP PYROPHOSPHATASE


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
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 131 TO ASN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 % / Description: NONE
Crystal growpH: 7
Details: 0.3 M AMMONIUM SULFATE, 25 % PEG 3350, 0.1 M HEPES PH 7, 10 MM DUTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BSY

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 1229 5.1 %RANDOM
Rwork0.19562 ---
obs0.1982 22791 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.495 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 35 225 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9852808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.46821.56683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02615333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.781519
X-RAY DIFFRACTIONr_chiral_restr0.1130.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2901
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21360
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0591.51274
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71622031
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6683870
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.094.5773
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 83 -
Rwork0.244 1688 -
obs--99.94 %

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