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- PDB-5hlj: Crystal Structure of Major Envelope Protein VP24 from White Spot ... -

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Basic information

Entry
Database: PDB / ID: 5hlj
TitleCrystal Structure of Major Envelope Protein VP24 from White Spot Syndrome Virus
ComponentsVP24
KeywordsVIRAL PROTEIN / WSSV / VP24 / envelope protein
Function / homologyWhite spot syndrome virus structural envelope protein Vp28 / WSSV envelope protein Vp28 superfamily / White spot syndrome virus structural envelope protein VP / membrane / VP24
Function and homology information
Biological speciesWhite spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.406 Å
AuthorsSun, L.F. / Su, Y.T. / Zhao, Y.H. / Fu, Z.Q. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31302225 China
CitationJournal: Sci Rep / Year: 2016
Title: Crystal Structure of Major Envelope Protein VP24 from White Spot Syndrome Virus
Authors: Sun, L.F. / Su, Y.T. / Zhao, Y.H. / Fu, Z.Q. / Wu, Y.K.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP24


Theoretical massNumber of molelcules
Total (without water)21,2561
Polymers21,2561
Non-polymers00
Water97354
1
A: VP24

A: VP24

A: VP24


Theoretical massNumber of molelcules
Total (without water)63,7683
Polymers63,7683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7110 Å2
ΔGint-28 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.735, 139.735, 139.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein VP24


Mass: 21255.947 Da / Num. of mol.: 1 / Fragment: UNP residues 30-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) White spot syndrome virus / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q80BF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 5.35 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, pH 8.5, 2.75 M NH4AC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 17758 / % possible obs: 99.9 % / Redundancy: 20.6 % / Biso Wilson estimate: 71.49 Å2 / Rmerge(I) obs: 0.074 / Net I/av σ(I): 51.361 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.4-2.4420.41100
2.44-2.4922.11100
2.49-2.5322.21100
2.53-2.5922.41100
2.59-2.6422.31100
2.64-2.722.311000.847
2.7-2.7722.311000.72
2.77-2.8522.311000.519
2.85-2.9322.411000.376
2.93-3.0222.111000.278
3.02-3.132211000.207
3.13-3.2621.611000.15
3.26-3.4121.111000.119
3.41-3.5920.411000.096
3.59-3.8119.311000.08
3.81-4.118.611000.068
4.1-4.5217.1199.80.059
4.52-5.1716.611000.054
5.17-6.5117.911000.052
6.51-10018198.80.043

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
SCALEPACKdata reduction
PHENIXphasing
RefinementStarting model: SAD

Resolution: 2.406→31.246 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 1760 9.93 %Random
Rwork0.1708 ---
obs0.173 17728 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.406→31.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 0 54 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081350
X-RAY DIFFRACTIONf_angle_d1.1251824
X-RAY DIFFRACTIONf_dihedral_angle_d13.688497
X-RAY DIFFRACTIONf_chiral_restr0.044207
X-RAY DIFFRACTIONf_plane_restr0.004238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4064-2.47140.29021360.30181213X-RAY DIFFRACTION100
2.4714-2.54410.34581330.27581213X-RAY DIFFRACTION100
2.5441-2.62620.29731380.26471220X-RAY DIFFRACTION100
2.6262-2.720.2721360.24241207X-RAY DIFFRACTION100
2.72-2.82880.24971300.23891223X-RAY DIFFRACTION100
2.8288-2.95750.25541320.22891217X-RAY DIFFRACTION100
2.9575-3.11330.2451390.21011219X-RAY DIFFRACTION100
3.1133-3.30810.22721360.20191216X-RAY DIFFRACTION100
3.3081-3.56320.20351390.18581252X-RAY DIFFRACTION100
3.5632-3.92120.19821310.17621221X-RAY DIFFRACTION100
3.9212-4.48710.15861380.15151236X-RAY DIFFRACTION100
4.4871-5.64790.13841350.1351244X-RAY DIFFRACTION100
5.6479-31.24830.18971370.14361287X-RAY DIFFRACTION99

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