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- PDB-3r6j: Crystal Structure of the Capsid P Domain from Norwalk Virus Strai... -

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Basic information

Entry
Database: PDB / ID: 3r6j
TitleCrystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999
ComponentsVP1 protein
KeywordsVIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA)
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 speciesNorwalk-like virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHansman, G.S. / Biertumpfel, C. / McLellan, J.S. / Georgiev, I. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2011
Title: Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.
Authors: Hansman, G.S. / Biertumpfel, C. / Georgiev, I. / McLellan, J.S. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: VP1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4772
Polymers33,4151
Non-polymers621
Water2,234124
1
A: VP1 protein
hetero molecules

A: VP1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9534
Polymers66,8292
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4050 Å2
ΔGint-5 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.154, 99.121, 77.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-24-

HOH

21A-47-

HOH

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Components

#1: Protein VP1 protein


Mass: 33414.504 Da / Num. of mol.: 1 / Fragment: unp residues 225-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk-like virus / Strain: Hiroshima/1999/JP / Gene: Capsid protein / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54AD6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Imidazole, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→24.78 Å / Num. obs: 28503 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 31.38 Å2 / Rsym value: 0.05 / Net I/σ(I): 28
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 2605 / Rsym value: 0.449 / % possible all: 92

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASER(2.1.4)phasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ONU

3onu


Resolution: 1.75→24.78 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1445 5.07 %RANDOM
Rwork0.1858 ---
all0.1858 28478 --
obs0.1867 28478 98.91 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0086 Å20 Å20 Å2
2--3.2789 Å20 Å2
3---7.6417 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 4 124 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042431
X-RAY DIFFRACTIONf_angle_d0.8373325
X-RAY DIFFRACTIONf_dihedral_angle_d11.602880
X-RAY DIFFRACTIONf_chiral_restr0.059366
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81250.3031130.25962489X-RAY DIFFRACTION92
1.8125-1.88510.25471630.22862641X-RAY DIFFRACTION98
1.8851-1.97080.26011360.21652704X-RAY DIFFRACTION100
1.9708-2.07470.23391350.20392710X-RAY DIFFRACTION100
2.0747-2.20460.22281440.19392741X-RAY DIFFRACTION100
2.2046-2.37470.21851690.19192664X-RAY DIFFRACTION100
2.3747-2.61340.23461530.19452728X-RAY DIFFRACTION100
2.6134-2.9910.22691480.2032732X-RAY DIFFRACTION100
2.991-3.76630.19851380.17152772X-RAY DIFFRACTION100
3.7663-24.78270.16961460.17242852X-RAY DIFFRACTION99
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)
12.2056-0.9162-0.59762.25011.22391.98640.032-0.0289-0.29180.03450.2136-0.28810.02470.4762-0.13090.171-0.0016-0.0170.284-0.06420.266910.804729.031614.3301
22.1192-0.5498-0.63582.73021.71731.71620.05680.0136-0.0272-0.14560.2005-0.2318-0.21260.3296-0.10730.194-0.03280.01120.2191-0.0560.16789.980635.39613.2269
33.0105-1.34130.51971.67020.69672.4493-0.22310.1318-1.1521-0.22570.12220.43230.0547-0.2407-0.05880.26750.0282-0.10520.428-0.24020.62670.251211.9303-0.4354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 225:328)
2X-RAY DIFFRACTION2(chain A and resid 329:460)
3X-RAY DIFFRACTION3(chain A and resid 461:525)

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