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- PDB-6ky8: Crystal structure of ASFV dUTPase -

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Basic information

Entry
Database: PDB / ID: 6ky8
TitleCrystal structure of ASFV dUTPase
ComponentsE165R
KeywordsHYDROLASE / dUTPase / ASFV / VIRAL PROTEIN
Function / homologydUTPase-like / dUTP diphosphatase / dUTPase / dUTP diphosphatase activity / dUTPase, trimeric / dUTPase-like superfamily / metal ion binding / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsLi, C. / Chai, Y. / Song, H. / Qi, J. / Sun, Y. / Gao, G.F.
CitationJournal: Mbio / Year: 2019
Title: Crystal Structure of African Swine Fever Virus dUTPase Reveals a Potential Drug Target.
Authors: Li, C. / Chai, Y. / Song, H. / Weng, C. / Qi, J. / Sun, Y. / Gao, G.F.
History
DepositionSep 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E165R


Theoretical massNumber of molelcules
Total (without water)19,1141
Polymers19,1141
Non-polymers00
Water79344
1
A: E165R

A: E165R

A: E165R


Theoretical massNumber of molelcules
Total (without water)57,3433
Polymers57,3433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4890 Å2
ΔGint-26 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.855, 97.855, 97.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

21A-242-

HOH

31A-243-

HOH

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Components

#1: Protein E165R / E165R CDS protein


Mass: 19114.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: E165R CDS, E165R, ASFV-Georgia_4-154 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A2X0SE53
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 39.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium citrate tribasic pH 7.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03923 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 7082 / % possible obs: 100 % / Redundancy: 38.6 % / CC1/2: 1 / Net I/σ(I): 53.9
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 690 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vyq

1vyq


Resolution: 2.301→39.949 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.25
RfactorNum. reflection% reflection
Rfree0.2547 398 5.62 %
Rwork0.2216 --
obs0.2236 7082 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 30.554 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 2.301→39.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 44 1201
Biso mean---30.36 -
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3014-2.63430.28041420.26822192
2.6343-3.31870.2961260.2612206
3.3-39.90.2231300.18772286

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