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- PDB-3bqj: VA387 polypeptide -

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Basic information

Entry
Database: PDB / ID: 3bqj
TitleVA387 polypeptide
Componentsva387 polypeptide
KeywordsVIRAL PROTEIN / va387 polypeptide (residues 230-529) / two folded units p1 and p2
Function / homologyPositive 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 / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta / Va387 polypeptide
Function and homology information
Biological speciesNorovirus isolates
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBu, W. / Mamedova, A. / Tan, M. / Jiang, J. / Hegde, R.
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
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: va387 polypeptide


Theoretical massNumber of molelcules
Total (without water)33,2031
Polymers33,2031
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: va387 polypeptide

A: va387 polypeptide


Theoretical massNumber of molelcules
Total (without water)66,4062
Polymers66,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.360, 96.800, 118.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein va387 polypeptide


Mass: 33203.008 Da / Num. of mol.: 1 / Fragment: p polypeptide (residues 225-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus isolates / Species: Norwalk virusNorovirus / Gene: VP1 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D0VWS6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE AT THE TIME OF PROCESSING.

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% peg 4k, 3% 5-diaminopentane, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 11, 2007 / Details: blue optics
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. obs: 11228 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Χ2: 1.125 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.383.10.23412011.0587.9
2.38-2.483.40.23212611.11389.7
2.48-2.593.50.21412411.11189.9
2.59-2.733.70.22912251.05697.8
2.73-2.93.60.1812091.15795.6
2.9-3.123.70.12311321.16491.1
3.12-3.443.50.08410311.28992.5
3.44-3.933.40.0639411.33396.3
3.93-4.963.10.0467451.22291.8
4.96-993.80.03212420.90791.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CNSphasing
DENZOdata reduction
RefinementResolution: 2.7→99 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.267 901 10.1 %
Rwork0.227 --
obs-8737 97.7 %
Solvent computationBsol: 40.94 Å2
Displacement parametersBiso mean: 38.662 Å2
Baniso -1Baniso -2Baniso -3
1--10.719 Å20 Å20 Å2
2--6.439 Å20 Å2
3---4.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 102 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3491.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2.3632
X-RAY DIFFRACTIONc_scangle_it2.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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