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- PDB-6ky9: Crystal structure of ASFV dUTPase and UMP complex -

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Basic information

Entry
Database: PDB / ID: 6ky9
TitleCrystal structure of ASFV dUTPase and UMP complex
ComponentsE165R
KeywordsHYDROLASE / Inhibitor / Complex. dUTPase / ASFV / E165R / VIRAL PROTEIN
Function / homologydUTPase-like / dUTP diphosphatase / dUTPase / dUTP diphosphatase activity / dUTPase, trimeric / dUTPase-like superfamily / metal ion binding / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: E165R
B: E165R
C: E165R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2686
Polymers57,3433
Non-polymers9253
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-43 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.418, 57.418, 149.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein E165R / E165R CDS protein


Mass: 19114.328 Da / Num. of mol.: 3
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: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


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


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric acid pH 3.5, 14% w/v Polyethylene glycol 1,000.

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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: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 1.696→50 Å / Num. obs: 53337 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.997 / Rpim(I) all: 0.03 / Net I/σ(I): 24.81
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.07 / Num. unique obs: 5306 / CC1/2: 0.997 / Rpim(I) all: 0.026

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vyq

1vyq


Resolution: 1.7→37.64 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.56
RfactorNum. reflection% reflection
Rfree0.2154 2643 4.97 %
Rwork0.1883 --
obs0.1897 53231 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.43 Å2 / Biso mean: 18.3329 Å2 / Biso min: 3.38 Å2
Refinement stepCycle: final / Resolution: 1.7→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 60 448 3886
Biso mean--16.74 26.94 -
Num. residues----432
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72710.27321510.2443257397
1.7271-1.76030.29331650.23932630100
1.7603-1.79620.2261250.22262691100
1.7962-1.83530.22411430.21932624100
1.8353-1.8780.24531340.21372658100
1.878-1.92490.2239960.21022715100
1.9249-1.9770.23211350.19552706100
1.977-2.03510.23261400.19782623100
2.0351-2.10080.22991130.1992674100
2.1008-2.17590.2441310.19332669100
2.1759-2.2630.23841600.19962657100
2.263-2.3660.24441400.21072663100
2.366-2.49070.21541340.20492675100
2.4907-2.64670.23331650.22625100
2.6467-2.8510.23121530.19412672100
2.851-3.13780.19111460.18382672100
3.1378-3.59150.18031600.16722652100
3.5915-4.52370.16771210.14842689100
4.5237-37.640.19971310.16072720100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06120.02370.00310.0115-0.00580.02070.0194-0.0220.0321-0.027-0.0428-0.0231-0.01190.0195-0.01810.0580.00980.02270.04190.00290.05078.7993-15.39938.6045
20.0151-0.0070.00360.0045-0.00780.0331-0.00450.022-0.0229-0.0729-0.03640.0250.0385-0.0222-0.06010.08890.0208-00.0472-0.0250.05873.128-40.85592.9452
30.0227-0.00090.00650.0251-0.00370.00230.0079-0.01130.003-0.0006-0.0301-0.05280.00870.0407-0.0180.04450.0126-0.01410.10310.03350.079917.9728-35.189223.7595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 144
2X-RAY DIFFRACTION2chain BB2 - 149
3X-RAY DIFFRACTION3chain CC2 - 201

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