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- PDB-3onu: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 -

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Basic information

Entry
Database: PDB / ID: 3onu
TitleCrystal Structure of P Domain from Norwalk Virus Strain Vietnam 026
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / viral capsid 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 speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.395 Å
AuthorsHansman, G.S. / Biertumpfel, C. / Chen, L. / Georgiev, I. / McLellan, J.S. / 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
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,93210
Polymers69,4362
Non-polymers4978
Water16,376909
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9665
Polymers34,7181
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9665
Polymers34,7181
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.217, 79.111, 69.292
Angle α, β, γ (deg.)90.00, 99.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein


Mass: 34717.879 Da / Num. of mol.: 2 / Fragment: P domain (UNP residues 225-538)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Strain: Vietnam 026 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F4T5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Imidazole pH 6.5, 8.25% PEG 8000, 1% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2010
RadiationMonochromator: SI 111. ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 130975 / Num. obs: 130975 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2 / Num. unique all: 9536 / % possible all: 69.6

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.395→22.695 Å / SU ML: 0.12 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1672 6166 5.04 %random
Rwork0.1505 ---
all0.1514 122330 --
obs0.1514 122330 88.91 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.481 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.379 Å2-0 Å2-2.3447 Å2
2---2.0272 Å20 Å2
3---3.4062 Å2
Refinement stepCycle: LAST / Resolution: 1.395→22.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 32 909 5755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114978
X-RAY DIFFRACTIONf_angle_d1.3316803
X-RAY DIFFRACTIONf_dihedral_angle_d11.5911785
X-RAY DIFFRACTIONf_chiral_restr0.084756
X-RAY DIFFRACTIONf_plane_restr0.008899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3955-1.41130.23511020.2242048X-RAY DIFFRACTION47
1.4113-1.42790.25011550.21972589X-RAY DIFFRACTION60
1.4279-1.44540.24041250.21492844X-RAY DIFFRACTION65
1.4454-1.46360.22941730.2052995X-RAY DIFFRACTION70
1.4636-1.48290.21521730.20453220X-RAY DIFFRACTION74
1.4829-1.50320.23421940.19573389X-RAY DIFFRACTION78
1.5032-1.52470.21522070.19143598X-RAY DIFFRACTION82
1.5247-1.54740.18421720.1773726X-RAY DIFFRACTION85
1.5474-1.57160.21122100.17673787X-RAY DIFFRACTION88
1.5716-1.59740.19422070.1673873X-RAY DIFFRACTION89
1.5974-1.62490.19782090.16293923X-RAY DIFFRACTION91
1.6249-1.65440.19272140.15713955X-RAY DIFFRACTION91
1.6544-1.68630.17862440.1513970X-RAY DIFFRACTION92
1.6863-1.72070.16371950.14784049X-RAY DIFFRACTION93
1.7207-1.75810.16832050.14224074X-RAY DIFFRACTION93
1.7581-1.79890.18792160.13774083X-RAY DIFFRACTION94
1.7989-1.84390.14262200.13724051X-RAY DIFFRACTION94
1.8439-1.89370.15352220.14634098X-RAY DIFFRACTION94
1.8937-1.94940.1642280.14354189X-RAY DIFFRACTION96
1.9494-2.01230.16592310.13924263X-RAY DIFFRACTION98
2.0123-2.08420.1552070.14034329X-RAY DIFFRACTION99
2.0842-2.16760.16662230.13874322X-RAY DIFFRACTION99
2.1676-2.26620.14942290.13344292X-RAY DIFFRACTION99
2.2662-2.38550.14072660.1354272X-RAY DIFFRACTION99
2.3855-2.53480.13832200.14034274X-RAY DIFFRACTION98
2.5348-2.73020.17572170.14754341X-RAY DIFFRACTION99
2.7302-3.00440.1612210.15114378X-RAY DIFFRACTION99
3.0044-3.43780.1652120.14834380X-RAY DIFFRACTION100
3.4378-4.32640.15592530.14224381X-RAY DIFFRACTION100
4.3264-22.69770.16842160.15874471X-RAY DIFFRACTION100
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)
10.65830.0724-0.03570.6807-0.06350.9128-0.01390.07980.0105-0.07060.03880.0095-0.08110.035-0.02670.0709-0.01130.00230.0649-0.00030.04078.12856.24428.662
20.8206-0.00110.1490.90130.10820.51650.0236-0.0279-0.11940.06940.0435-0.16030.03590.0789-0.05590.07460.0063-0.02140.0785-0.00760.105720.7727-5.910325.0878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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