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- PDB-3by2: Norwalk P polypeptide (228-523) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3by2
TitleNorwalk P polypeptide (228-523)
Components58 kd capsid protein
KeywordsVIRAL PROTEIN / Norwalk Virus P polypeptide
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHegde, R. / Bu, W.
CitationJournal: J.Virol. / Year: 2008
Title: Structural basis for the receptor binding specificity of Norwalk virus.
Authors: Bu, W. / Mamedova, A. / Tan, M. / Xia, M. / Jiang, X. / Hegde, R.S.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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: 58 kd capsid protein


Theoretical massNumber of molelcules
Total (without water)32,5281
Polymers32,5281
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 58 kd capsid protein

A: 58 kd capsid protein


Theoretical massNumber of molelcules
Total (without water)65,0572
Polymers65,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area3100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.799, 83.771, 102.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein 58 kd capsid protein


Mass: 32528.453 Da / Num. of mol.: 1 / Fragment: UNP residues 218-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Genus: Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q83884
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.72 Å3/Da / Density % sol: 54.86 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 8335 / Num. obs: 8083 / Redundancy: 1.9 % / Rsym value: 0.055

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ihm

1ihm


Resolution: 2.6→50 Å / Cross valid method: procheck
RfactorNum. reflection
Rfree0.2708 861
Rwork0.2124 -
all-8335
obs-8083
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 0 106 2220

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