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- PDB-4oox: Crystal structure of P domain from norovirus strain Saga4 -

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Basic information

Entry
Database: PDB / ID: 4oox
TitleCrystal structure of P domain from norovirus strain Saga4
ComponentsVP1
KeywordsVIRAL PROTEIN / VIRAL CAPSID PROTEIN / Protruding domain
Function / homology
Function and homology information


virion component / host cell cytoplasm
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 speciesNorovirus Hu/GII-4/Kumamoto5/2006/JP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,55511
Polymers33,9401
Non-polymers61510
Water5,314295
1
A: VP1
hetero molecules

A: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,10922
Polymers67,8802
Non-polymers1,22920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6700 Å2
ΔGint15 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.720, 58.940, 62.140
Angle α, β, γ (deg.)90.000, 119.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-828-

HOH

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Components

#1: Protein VP1


Mass: 33939.953 Da / Num. of mol.: 1 / Fragment: unp residues 225-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII-4/Kumamoto5/2006/JP / Gene: AB447457 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5BTT5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Sodium acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97243 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 1.03→96.0295 Å / Num. obs: 135999 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 10.78 Å2 / Rmerge(I) obs: 0.034 / Χ2: 0.949 / Net I/σ(I): 15.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.03-1.060.5481.825530976089.4
1.06-1.090.3882.7128002984391.5
1.09-1.120.2863.6828212972793.1
1.12-1.150.2194.7127044950393.9
1.15-1.190.1825.4325194932194.9
1.19-1.230.1516.9228052926296.7
1.23-1.280.137.8727045891897.3
1.28-1.330.1069.4626001861097.8
1.33-1.390.08511.224200831897.8
1.39-1.460.0713.4723011789597.6
1.46-1.540.05617.2723885757798.5
1.54-1.630.04520.8922547721698.5
1.63-1.740.03724.4120850677898.6
1.74-1.880.03128.4317838623097.1
1.88-2.060.02534.817390575097.6
2.06-2.30.02339.7816787526298.5
2.3-2.660.02342.214662462597.7
2.66-3.260.02343.8111644389997.5
3.26-4.610.02746.978975297895.4
4.610.02949.15476168695.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→27.173 Å / FOM work R set: 0.9456 / SU ML: 0.07 / σ(F): 1.37 / Phase error: 11.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1432 4625 5 %
Rwork0.1196 --
obs0.1208 135999 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.16 Å2 / Biso mean: 15.38 Å2 / Biso min: 6.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 40 295 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092549
X-RAY DIFFRACTIONf_angle_d1.3633482
X-RAY DIFFRACTIONf_chiral_restr0.087381
X-RAY DIFFRACTIONf_plane_restr0.008461
X-RAY DIFFRACTIONf_dihedral_angle_d12.473925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.15381500.1142855300597
1.2136-1.22790.13781530.1082911306497
1.2279-1.24290.12071530.10622900305398
1.2429-1.25860.16741540.10662917307197
1.2586-1.27520.14421520.10282896304898
1.2752-1.29270.13711530.0982898305197
1.2927-1.31110.13371520.09982906305898
1.3111-1.33070.12451560.09522954311098
1.3307-1.35150.12941540.09712920307498
1.3515-1.37360.13421530.09882907306098
1.3736-1.39730.12481530.09762910306398
1.3973-1.42270.1381530.09612903305696
1.4227-1.45010.12131550.09312955311099
1.4501-1.47970.12491560.09312963311999
1.4797-1.51190.10431530.09162907306099
1.5119-1.5470.1261550.09092950310598
1.547-1.58570.13091540.08952927308199
1.5857-1.62860.12821560.09212961311799
1.6286-1.67650.11911560.09692965312199
1.6765-1.73060.141570.1012967312499
1.7306-1.79240.13541540.10542928308299
1.7924-1.86420.1291510.10872868301996
1.8642-1.9490.13181530.1112924307797
1.949-2.05170.14531560.11012946310299
2.0517-2.18020.14081570.11352993315099
2.1802-2.34850.14581550.11932952310799
2.3485-2.58470.15311550.13412945310098
2.5847-2.95830.1561560.1482951310798
2.9583-3.72560.16161520.13932900305296
3.7256-27.18020.15481580.14793000315897

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