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- PDB-7vp0: Crystal structure of P domain from norovirus GI.9 capsid protein. -

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Basic information

Entry
Database: PDB / ID: 7vp0
TitleCrystal structure of P domain from norovirus GI.9 capsid protein.
ComponentsVP1
KeywordsVIRAL PROTEIN / norovirus / p-domain / capsid
Function / homology
Function and homology information


virion component / host cell cytoplasm / metal ion binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesNorovirus Hu/GI/Vancouver730/2004/CAN
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKatsura, K. / Sakai, N. / Hasegawa, K. / Kimura-Someya, T. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Febs Open Bio / Year: 2022
Title: Lewis fucose is a key moiety for the recognition of histo-blood group antigens by GI.9 norovirus, as revealed by structural analysis.
Authors: Kimura-Someya, T. / Kato-Murayama, M. / Katsura, K. / Sakai, N. / Murayama, K. / Hanada, K. / Shirouzu, M. / Someya, Y.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6044
Polymers67,5562
Non-polymers492
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-34 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.950, 103.550, 76.910
Angle α, β, γ (deg.)90.000, 116.660, 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
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

21A-838-

HOH

31A-855-

HOH

41B-803-

HOH

51B-842-

HOH

61B-871-

HOH

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Components

#1: Protein VP1


Mass: 33777.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI/Vancouver730/2004/CAN / Production host: Escherichia coli (E. coli) / References: UniProt: F2XMU3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 4.5 Å3/Da / Density % sol: 72.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.10M BICINE (pH 9), 1.70M Magnesium chloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.04 Å / Num. obs: 134729 / % possible obs: 98.1 % / Redundancy: 1.95 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.44
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 21576 / CC1/2: 0.368

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Processing

Software
NameVersionClassification
XDSVERSION Nov 1, 2016 BUILT=20170215data scaling
PHASER2.7.17phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rdj

4rdj


Resolution: 2.1→48.04 Å / SU ML: 0.4276 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 34.9323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 6767 5.04 %
Rwork0.2373 127630 -
obs0.2389 134397 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 2 334 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834876
X-RAY DIFFRACTIONf_angle_d0.95596702
X-RAY DIFFRACTIONf_chiral_restr0.0569750
X-RAY DIFFRACTIONf_plane_restr0.0089898
X-RAY DIFFRACTIONf_dihedral_angle_d7.1975654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.48612130.44953998X-RAY DIFFRACTION89.9
2.13-2.150.4621900.43034248X-RAY DIFFRACTION98.84
2.15-2.180.4092640.42094276X-RAY DIFFRACTION98.46
2.18-2.210.44952300.41734261X-RAY DIFFRACTION98.59
2.21-2.240.44992270.39654217X-RAY DIFFRACTION98.43
2.24-2.270.47952220.45184197X-RAY DIFFRACTION95.71
2.27-2.30.42952760.3764126X-RAY DIFFRACTION97.91
2.3-2.330.3873080.37644282X-RAY DIFFRACTION98.6
2.33-2.370.38032550.34664205X-RAY DIFFRACTION98.48
2.37-2.410.3712020.35084274X-RAY DIFFRACTION98.98
2.41-2.450.32922250.3414324X-RAY DIFFRACTION98.93
2.45-2.490.35042350.34854305X-RAY DIFFRACTION99.1
2.49-2.540.3422420.32424268X-RAY DIFFRACTION99.4
2.54-2.590.36912670.3154225X-RAY DIFFRACTION98.83
2.59-2.650.412150.3014289X-RAY DIFFRACTION99.05
2.65-2.710.33652040.28884305X-RAY DIFFRACTION98.21
2.71-2.780.3082350.29454306X-RAY DIFFRACTION98.89
2.78-2.850.29862550.27464310X-RAY DIFFRACTION98.79
2.85-2.940.31131990.26284336X-RAY DIFFRACTION99.15
2.94-3.030.27112370.24734195X-RAY DIFFRACTION99.06
3.03-3.140.23872310.2374315X-RAY DIFFRACTION98.89
3.14-3.270.28472200.22134223X-RAY DIFFRACTION98.65
3.27-3.420.24711780.22334354X-RAY DIFFRACTION98.84
3.42-3.60.22511960.21374274X-RAY DIFFRACTION97.7
3.6-3.820.2212140.19314221X-RAY DIFFRACTION97.39
3.82-4.120.19922090.17124265X-RAY DIFFRACTION97.6
4.12-4.530.1821980.14184315X-RAY DIFFRACTION98.13
4.53-5.190.17531870.14994246X-RAY DIFFRACTION97.84
5.19-6.530.18012180.17934224X-RAY DIFFRACTION97.58
6.53-48.040.2082150.18544246X-RAY DIFFRACTION97.44

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