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- PDB-8rt0: BTV-15 VP5 pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 8rt0
TitleBTV-15 VP5 pH 6.0
ComponentsOuter capsid protein VP5
KeywordsVIRAL PROTEIN / Bluetongue 15 VP5 Outer capsid protein pH 6.0
Function / homologyOuter capsid protein VP5, Orbivirus / Orbivirus outer capsid protein VP5 / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / structural molecule activity / Outer capsid protein VP5
Function and homology information
Biological speciesBluetongue virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsStuart, D.I. / Sutton, G.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)G1000099 United Kingdom
CitationJournal: J.Gen.Virol. / Year: 2024
Title: The effect of pH on the structure of Bluetongue virus VP5.
Authors: Zhang, H. / El Omari, K. / Sutton, G. / Stuart, D.I.
History
DepositionJan 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer capsid protein VP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2842
Polymers55,2221
Non-polymers621
Water1448
1
A: Outer capsid protein VP5
hetero molecules

A: Outer capsid protein VP5
hetero molecules

A: Outer capsid protein VP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,8516
Polymers165,6653
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9660 Å2
ΔGint-61 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.870, 76.870, 163.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-708-

HOH

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Components

#1: Protein Outer capsid protein VP5


Mass: 55221.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bluetongue virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4J9Y2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1M Sodium Chloride, 0.1M Tris, pH 6.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 2.19→51.8 Å / Num. obs: 18479 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 55.96 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 1322 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→51.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.919 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22908 869 4.7 %RANDOM
Rwork0.19919 ---
obs0.20069 17608 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.066 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0.76 Å20 Å2
2---1.52 Å20 Å2
3---4.92 Å2
Refinement stepCycle: 1 / Resolution: 2.19→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 0 8 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.8352523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.969515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32210328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1470.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021427
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.3736.407893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.63411.4791111
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.867.246982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.74583.967745
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 64 -
Rwork0.314 1256 -
obs--100 %

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