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- PDB-7cp2: Crystal structure of the African swine fever virus core shell pro... -

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Basic information

Entry
Database: PDB / ID: 7cp2
TitleCrystal structure of the African swine fever virus core shell protein p15
ComponentsCP530R
KeywordsVIRAL PROTEIN / African swine fever virus (ASFV) / p15 / trimer / VIRUS
Function / homologyviral capsid assembly / virion component / host cell perinuclear region of cytoplasm / Polyprotein pp62 / CP530R
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsLiu, K.F. / Meng, Y.M. / Chai, Y. / Li, L.J. / Sun, H. / Gao, G.F. / Tan, S.G. / Qi, J.X.
CitationJournal: Biosaf Health / Year: 2021
Title: Crystal structure of the African swine fever virus core shell protein p15
Authors: Liu, K.F. / Meng, Y.M. / Chai, Y. / Li, L.J. / Sun, H. / Gao, G.F. / Tan, S.G. / Qi, J.X.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _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: CP530R
B: CP530R
C: CP530R


Theoretical massNumber of molelcules
Total (without water)51,4233
Polymers51,4233
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-24 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.037, 53.601, 74.892
Angle α, β, γ (deg.)90.000, 92.890, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein CP530R / CP530R CDS protein / CP530R protein / Pp62


Mass: 17140.889 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: CP530R, CP530R CDS, ASFV-Georgia_4-118 / Production host: Escherichia coli (E. coli) / References: UniProt: X2L313, UniProt: Q65179*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03836 Å
DetectorType: SDMS / Detector: CMOS / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03836 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 25170 / % possible obs: 98.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.11 Å2 / Rrim(I) all: 0.093 / Net I/σ(I): 21.02
Reflection shellResolution: 2.19→2.28 Å / Rmerge(I) obs: 0.836 / Num. unique obs: 2482

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→46.79 Å / SU ML: 0.2846 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2461 1135 4.71 %
Rwork0.2188 22957 -
obs0.22 24092 93.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.35 Å2
Refinement stepCycle: LAST / Resolution: 2.19→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 0 162 3646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223569
X-RAY DIFFRACTIONf_angle_d0.46054834
X-RAY DIFFRACTIONf_chiral_restr0.0418536
X-RAY DIFFRACTIONf_plane_restr0.0047617
X-RAY DIFFRACTIONf_dihedral_angle_d18.90991359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.290.3168810.28851934X-RAY DIFFRACTION62.97
2.29-2.410.33891230.26932710X-RAY DIFFRACTION88.31
2.41-2.560.31821380.2673044X-RAY DIFFRACTION98.97
2.56-2.750.31711480.26483035X-RAY DIFFRACTION99.41
2.75-3.030.27691690.24752978X-RAY DIFFRACTION97.4
3.03-3.470.29261470.23443070X-RAY DIFFRACTION99.54
3.47-4.370.19921520.18293063X-RAY DIFFRACTION98.47
4.37-46.790.18541770.17733123X-RAY DIFFRACTION98.92

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