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- PDB-7c5z: Crystal structure of spring viremia of carp virus phosphoprotein ... -

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Basic information

Entry
Database: PDB / ID: 7c5z
TitleCrystal structure of spring viremia of carp virus phosphoprotein central domain
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / SVCV / P protein / Central domain / dimer
Function / homologyPhosphoprotein, C-terminal domain, viral / Phosphoprotein
Function and homology information
Biological speciesSpring viremia of carp virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsWang, Z.X. / Guan, H.X. / Ouyang, S.Y. / Zhang, Y.A.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)31725026 China
National Science Foundation (NSF, United States)31770948 China
National Science Foundation (NSF, United States)31570875 China
CitationJournal: J.Virol. / Year: 2020
Title: Structural and Functional Characterization of the Phosphoprotein Central Domain of Spring Viremia of Carp Virus.
Authors: Wang, Z.X. / Liu, S.B. / Guan, H. / Lu, L.F. / Tu, J.G. / Ouyang, S. / Zhang, Y.A.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)19,5372
Polymers19,5372
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-32 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.900, 54.110, 89.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phosphoprotein


Mass: 9768.437 Da / Num. of mol.: 2 / Fragment: central domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spring viremia of carp virus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7J936
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17% PEG 10000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→34.93 Å / Num. obs: 30365 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 22.56 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 2184 / CC1/2: 0.673 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→34.92 Å / SU ML: 0.1747 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 1473 4.86 %
Rwork0.207 28831 -
obs0.2079 30304 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 62 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571334
X-RAY DIFFRACTIONf_angle_d0.79941802
X-RAY DIFFRACTIONf_chiral_restr0.0567182
X-RAY DIFFRACTIONf_plane_restr0.0046238
X-RAY DIFFRACTIONf_dihedral_angle_d2.6532774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.31391480.24532559X-RAY DIFFRACTION100
1.55-1.60.26081280.23772577X-RAY DIFFRACTION100
1.6-1.670.28131120.24652588X-RAY DIFFRACTION100
1.67-1.740.26761320.25652598X-RAY DIFFRACTION100
1.74-1.840.26151480.23132569X-RAY DIFFRACTION100
1.84-1.950.21931300.20442607X-RAY DIFFRACTION100
1.95-2.10.21491410.19832606X-RAY DIFFRACTION100
2.1-2.310.22891270.19832612X-RAY DIFFRACTION100
2.31-2.650.19851370.20362638X-RAY DIFFRACTION100
2.65-3.340.21531330.21412678X-RAY DIFFRACTION100
3.34-34.920.22241370.19512799X-RAY DIFFRACTION100

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