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- PDB-4quz: Crystal structure of Feline Norovirus P Domain -

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Basic information

Entry
Database: PDB / ID: 4quz
TitleCrystal structure of Feline Norovirus P Domain
ComponentsVP1
KeywordsVIRAL PROTEIN / Feline Norovirus / Viral capsid protein / P domain / Protruding domain
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
Biological speciesNorovirus cat/GIV.2/CU081210E/USA/2010
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: Virology / Year: 2015
Title: Structural analysis of a feline norovirus protruding domain.
Authors: Singh, B.K. / Glatt, S. / Ferrer, J.L. / Koromyslova, A.D. / Leuthold, M.M. / Dunder, J. / Hansman, G.S.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6367
Polymers73,3262
Non-polymers3105
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint1 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.740, 99.920, 59.610
Angle α, β, γ (deg.)90.000, 97.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 225 - 565 / Label seq-ID: 1 - 341

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN AAA
2CHAIN BBB

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Components

#1: Protein VP1


Mass: 36662.984 Da / Num. of mol.: 2 / Fragment: P domain (UNP RESIDUES 225-565)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus cat/GIV.2/CU081210E/USA/2010 / Gene: JF781268 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8YRY9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, Glycerol, 2-propanol, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979738 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979738 Å / Relative weight: 1
ReflectionResolution: 2.1→49.634 Å / Num. obs: 37583 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 19.64 Å2 / Rmerge(I) obs: 0.204 / Χ2: 0.937 / Net I/σ(I): 5.26
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.160.6140.7651.385241286621370.95674.6
2.16-2.220.710.7171.728135281227880.8899.1
2.22-2.280.7370.5572.517713270626390.68497.5
2.28-2.350.7950.7771.87706264425720.94897.3
2.35-2.430.8080.572.137605254025270.69699.5
2.43-2.520.780.6092.287374249024650.74499
2.52-2.610.8130.5532.47221238123680.67399.5
2.61-2.720.8860.4132.986950229522770.50399.2
2.72-2.840.9150.3563.356758221322000.43399.4
2.84-2.980.9180.3173.886487212521070.38599.2
2.98-3.140.9570.2155.326053199419740.26299
3.14-3.330.9680.167.15793190818880.19499
3.33-3.560.980.1268.535209176617380.15498.4
3.56-3.840.9790.1119.814723169116220.13795.9
3.84-4.210.9870.09111.054440152214740.11296.8
4.21-4.710.9930.06713.544246138613590.0898.1
4.71-5.430.9920.06513.973807123512100.07998
5.43-6.660.9930.06413.573281105310330.07798.1
6.66-9.410.9950.05415.1425188077960.06598.6
9.410.9940.04718.1412204694090.05787.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.16 Å49.63 Å
Translation2.16 Å49.63 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: 2.35→49.634 Å / FOM work R set: 0.8016 / SU ML: 0.3 / σ(F): 1.99 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1378 5 %
Rwork0.2143 --
obs0.2169 27538 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.17 Å2 / Biso mean: 38.67 Å2 / Biso min: 14.05 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 20 206 5013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044938
X-RAY DIFFRACTIONf_angle_d0.8326746
X-RAY DIFFRACTIONf_chiral_restr0.033738
X-RAY DIFFRACTIONf_plane_restr0.006895
X-RAY DIFFRACTIONf_dihedral_angle_d13.7791749
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2840X-RAY DIFFRACTION5.648TORSIONAL
12B2840X-RAY DIFFRACTION5.648TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.4340.29031380.25162615275399
2.434-2.53150.30891380.27232627276599
2.5315-2.64670.32941380.25652619275799
2.6467-2.78620.30781390.25762634277399
2.7862-2.96070.31121390.25992634277399
2.9607-3.18930.25881370.23352622275999
3.1893-3.51020.28231380.21012625276399
3.5102-4.01790.26991350.21122555269096
4.0179-5.06130.20471370.15852607274498
5.0613-49.6450.22051390.16492622276197
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)
10.4832-0.05160.21460.9799-0.00271.1812-0.01690.02980.0401-0.0176-0.01040.1822-0.00860.0280.0120.2138-0.0029-0.03980.2747-0.00410.538444.31679.0108116.8819
22.68960.1530.73551.2685-0.09791.0457-0.1232-0.35010.45440.31080.06220.2542-0.0521-0.14470.07470.30840.06740.00780.3284-0.07220.375445.099121.9535133.6037
30.5891-0.3752-0.351.3780.38490.8965-0.00220.1331-0.1597-0.1244-0.02950.28710.1223-0.05750.0180.2251-0.0278-0.03830.2826-0.01470.404541.941.4062112.0804
40.28240.087-0.05360.7737-0.19720.6827-0.0444-0.1062-0.16510.06650.0134-0.19440.0876-0.00380.03350.17410.0089-0.01850.26320.00570.352266.40155.927124.3024
51.5236-0.2409-0.46831.4223-0.03690.9789-0.1068-0.2765-0.04420.24630.0786-0.2540.02120.13310.03970.29540.0632-0.0750.33660.0220.409967.18972.0086134.053
60.4285-0.31740.27181.5598-0.35281.46490.03020.04990.2561-0.084-0.1187-0.2811-0.14070.07470.07990.22110.0012-0.01540.3070.02260.435669.618720.1543111.994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 225:285 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 286:453 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 454:565 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 225:345 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 346:453 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 454:565 )

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