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- PDB-4oos: Crystal structure of P domain from norovirus strain NSW0514 -

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Basic information

Entry
Database: PDB / ID: 4oos
TitleCrystal structure of P domain from norovirus strain NSW0514
ComponentsVP1
KeywordsVIRAL PROTEIN / VIRAL CAPSID PROTEIN
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/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 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)34,5927
Polymers34,2191
Non-polymers3726
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.480, 55.070, 63.460
Angle α, β, γ (deg.)90.000, 120.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-990-

HOH

21A-1009-

HOH

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Components

#1: Protein VP1


Mass: 34219.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Gene: JX459908 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K4LM89
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Sodium formate, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978174 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978174 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 38171 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 10.54 Å2 / Rmerge(I) obs: 0.044 / Χ2: 1.001 / Net I/σ(I): 20.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.640.2475.048797270694
1.64-1.690.216.259695270597.1
1.69-1.740.1767.389430262597.4
1.74-1.790.1468.929266259597.8
1.79-1.850.11910.858940249497.5
1.85-1.910.09512.998642241897.9
1.91-1.980.07815.748356234698
1.98-2.070.0718.467839225397.4
2.07-2.160.05620.977774218598.2
2.16-2.260.04823.957341208098.6
2.26-2.390.04325.67099199498.9
2.39-2.530.0427.256672188599
2.53-2.70.03629.776244176998.9
2.7-2.920.03233.045905167599.2
2.92-3.20.02837.885355153299.3
3.2-3.580.02542.374764137599
3.58-4.130.02345.034093121798.5
4.13-5.060.0247.683690105799.3
5.06-7.160.01945.62286681999
7.160.01746.76148044193.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.35 Å41.77 Å
Translation1.35 Å41.77 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→42.599 Å / FOM work R set: 0.9244 / SU ML: 0.11 / σ(F): 2 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1615 1779 5 %
Rwork0.1377 --
obs0.1389 35573 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.94 Å2 / Biso mean: 14.18 Å2 / Biso min: 4.62 Å2
Refinement stepCycle: LAST / Resolution: 1.64→42.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 24 313 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052494
X-RAY DIFFRACTIONf_angle_d1.093400
X-RAY DIFFRACTIONf_chiral_restr0.065373
X-RAY DIFFRACTIONf_plane_restr0.005451
X-RAY DIFFRACTIONf_dihedral_angle_d12.145893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.68440.1881340.14412550268497
1.6844-1.73390.17151340.14472545267997
1.7339-1.78990.17691360.13962581271798
1.7899-1.85390.17531340.13462559269398
1.8539-1.92810.16871360.132584272098
1.9281-2.01590.14491360.12822575271198
2.0159-2.12210.13351360.12522594273098
2.1221-2.25510.15181370.12642604274199
2.2551-2.42920.1681370.13432605274299
2.4292-2.67360.18361390.142637277699
2.6736-3.06040.14381390.140426312770100
3.0604-3.85540.17071390.14022637277699
3.8554-42.61310.15651420.14782692283499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4244-0.1171-0.05310.173-0.02780.2883-0.0227-0.0305-0.0307-0.0153-0.0017-0.00130.0315-0.0014-00.0644-0.00050.00130.06380.00410.061102.3286-26.778210.6578
20.3516-0.02740.01590.0155-0.0670.2816-0.0187-0.03990.07390.00850.04180.1016-0.0858-0.0923-00.08970.0070.01660.085-0.00440.117384.0336-10.63310.1617
30.2190.0509-0.15560.14110.06690.18670.00050.03150.10360.0125-0.0235-0.005-0.09090.03240.03460.0790.0039-0.00180.06970.00550.080591.0792-4.92063.8697
40.1236-0.04290.01760.03760.04560.1207-0.05-0.00620.10940.04290.03970.0373-0.2063-0.1146-0.01690.11260.02650.00230.0907-0.0030.119586.8097-3.349710.311
50.0914-0.0603-0.06360.2229-0.06710.09930.0041-0.16350.09130.2234-0.0055-0.0261-0.24780.03390.04010.1691-0.0255-0.02910.1169-0.02430.0898103.4172-4.466211.7041
60.4897-0.0628-0.01220.3257-0.03820.3195-0.0268-0.1022-0.03150.04650.0222-0.01590.00390.02230.00040.0670.00050.00090.07840.00890.0493104.6266-25.067114.6217
70.07750.01740.00870.19730.10280.05950.0224-0.0249-0.01510.0650.0253-0.03170.03470.06940.04350.08280.0071-0.00670.10380.01490.0976114.7642-31.192314.0578
80.05990.0182-0.02780.079-0.06130.0589-0.0245-0.0744-0.08860.05580.0385-0.12940.1530.0140.01370.11430.02120.00130.10790.02630.1191112.5616-40.571715.607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 285 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 323 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 324 through 352 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 353 through 380 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 398 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 399 through 484 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 485 through 513 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 514 through 530 )A0

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