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- PDB-6lis: ASFV dUTPase in complex with dUMP -

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Basic information

Entry
Database: PDB / ID: 6lis
TitleASFV dUTPase in complex with dUMP
ComponentsE165R
KeywordsVIRUS / ASFV / aDUT / dUTPase / dUMP
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / virion component / host cell cytoplasm / metal ion binding
Similarity search - Function
dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsLiang, R. / Peng, G.Q.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development.
Authors: Liang, R. / Wang, G. / Zhang, D. / Ye, G. / Li, M. / Shi, Y. / Shi, J. / Chen, H. / Peng, G.
History
DepositionDec 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: E165R
B: E165R
C: E165R
D: E165R
E: E165R
F: E165R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,56212
Polymers109,7136
Non-polymers1,8496
Water8,647480
1
A: E165R
B: E165R
C: E165R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7816
Polymers54,8563
Non-polymers9253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-41 kcal/mol
Surface area18180 Å2
MethodPISA
2
D: E165R
E: E165R
F: E165R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7816
Polymers54,8563
Non-polymers9253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-38 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.179, 103.060, 102.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
E165R / E165R CDS protein


Mass: 18285.447 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus
Gene: E165R CDS, E165R, ASFV-Georgia_4-154, ASFV_Kyiv_2016_131_00207
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X0SE53, UniProt: Q65199*PLUS
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate, 0.1 m, 24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.998→30.61 Å / Num. obs: 69859 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.994 / CC star: 0.998 / Χ2: 1.009 / Net I/σ(I): 2.68
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.24 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 6889 / CC1/2: 0.883 / CC star: 0.969 / Rpim(I) all: 0.2 / Rrim(I) all: 0.709 / Χ2: 0.948 / % possible all: 100

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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: 2HQU

2hqu


Resolution: 1.998→30.608 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.23
RfactorNum. reflection% reflection
Rfree0.226 2025 2.91 %
Rwork0.1873 --
obs0.1885 69483 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.19 Å2 / Biso mean: 26.8441 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: final / Resolution: 1.998→30.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 120 480 7308
Biso mean--33.21 30.02 -
Num. residues----859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9985-2.04850.29551370.2469461596
2.0485-2.10380.28311430.22734769100
2.1038-2.16570.26911420.21714760100
2.1657-2.23560.25841380.21174845100
2.2356-2.31550.2211540.21064713100
2.3155-2.40810.23631390.20774818100
2.4081-2.51770.23461350.20574842100
2.5177-2.65040.23631490.19624809100
2.6504-2.81630.23631490.20214811100
2.8163-3.03360.25991410.19844846100
3.0336-3.33850.21431410.18494849100
3.3385-3.82080.18111530.16894876100
3.8208-4.81080.2051490.14954916100
4.8108-100.22521550.1772498998

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