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- PDB-5ysx: Structure of P domain of GII.2 Noroviruses -

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Basic information

Entry
Database: PDB / ID: 5ysx
TitleStructure of P domain of GII.2 Noroviruses
ComponentsVP1
KeywordsCELL ADHESION / GII.2 Noroviruses / P dimer
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Capsid protein / VP1
Similarity search - Component
Biological speciesNorovirus GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.202 Å
AuthorsDuan, Z. / Ao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Special National Project on Research and Development of Key Biosafety TechnologiesGrant No. 2016YFC1201900 China
CitationJournal: J. Infect. Dis. / Year: 2018
Title: Genetic Analysis of Reemerging GII.P16-GII.2 Noroviruses in 2016-2017 in China.
Authors: Ao, Y. / Cong, X. / Jin, M. / Sun, X. / Wei, X. / Wang, J. / Zhang, Q. / Song, J. / Yu, J. / Cui, J. / Qi, J. / Tan, M. / Duan, Z.
History
DepositionNov 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1


Theoretical massNumber of molelcules
Total (without water)34,1491
Polymers34,1491
Non-polymers00
Water7,584421
1
A: VP1

A: VP1


Theoretical massNumber of molelcules
Total (without water)68,2982
Polymers68,2982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
Unit cell
Length a, b, c (Å)96.534, 96.534, 64.319
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein VP1


Mass: 34149.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: A0A1X9W7M5, UniProt: A0A2R3BZ02*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 4.6
Details: 0.1 M Sodium Acetate trihydrate pH 4.6, 8% w/v Polyethylene Glycol 4000

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 99924 / % possible obs: 99.7 % / Redundancy: 12.1 % / Net I/σ(I): 29.5
Reflection shellResolution: 1.2→1.24 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RPB

4rpb


Resolution: 1.202→28.361 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.02
RfactorNum. reflection% reflection
Rfree0.1671 5012 5.02 %
Rwork0.154 --
obs0.1547 99924 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.06 Å2 / Biso mean: 24.0283 Å2 / Biso min: 8.63 Å2
Refinement stepCycle: final / Resolution: 1.202→28.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 0 421 2833
Biso mean---33.41 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092504
X-RAY DIFFRACTIONf_angle_d1.0793434
X-RAY DIFFRACTIONf_chiral_restr0.089375
X-RAY DIFFRACTIONf_plane_restr0.008462
X-RAY DIFFRACTIONf_dihedral_angle_d18.065903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6789-1.73310.16021910.14913372
2.1834-2.35190.16181530.1443440
2.9626-3.73120.16131740.14313487
Refinement TLS params.Method: refined / Origin x: 25.8021 Å / Origin y: -38.8937 Å / Origin z: 10.3564 Å
111213212223313233
T0.1271 Å2-0.031 Å2-0.0031 Å2-0.114 Å20.0017 Å2--0.102 Å2
L0.4305 °20.2025 °2-0.0331 °2-0.5361 °20.1441 °2--0.6568 °2
S-0.0707 Å °0.0632 Å °0.0063 Å °-0.1301 Å °0.0511 Å °-0.0315 Å °-0.0773 Å °0.003 Å °-0.0224 Å °
Refinement TLS groupSelection details: all

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