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- PDB-3q6r: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 0... -

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Basic information

Entry
Database: PDB / ID: 3q6r
TitleCrystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with disordered HBGA type Lex
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA)
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
IMIDAZOLE / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHansman, G.S. / Biertumpfel, C. / McLellan, J.S. / Chen, L. / Georgiev, I. / 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
DepositionJan 3, 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_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)71,06625
Polymers69,6102
Non-polymers1,45623
Water17,421967
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-13 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.280, 79.024, 69.703
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit is also biological unit.

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Components

#1: Protein Capsid protein


Mass: 34804.953 Da / Num. of mol.: 2 / Fragment: unp residues 225-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Strain: Vietnam 026 / Gene: Capsid protein / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F4T5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 51.66 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5

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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: Aug 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→26.674 Å / Num. all: 136423 / Num. obs: 136423 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 22.17
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.67 % / Mean I/σ(I) obs: 2.39 / Num. unique all: 36943 / Rsym value: 0.71 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASER(2.1.4)phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ONU

3onu


Resolution: 1.4→26.674 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 6924 5.08 %RANDOM
Rwork0.1648 ---
all0.1654 136413 --
obs0.1654 136413 99.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.607 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.6254 Å2-0 Å2-2.5603 Å2
2---1.2109 Å20 Å2
3---2.8362 Å2
Refinement stepCycle: LAST / Resolution: 1.4→26.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 96 967 5856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065047
X-RAY DIFFRACTIONf_angle_d1.0626867
X-RAY DIFFRACTIONf_dihedral_angle_d11.7651807
X-RAY DIFFRACTIONf_chiral_restr0.074759
X-RAY DIFFRACTIONf_plane_restr0.005906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4-1.41590.27812440.264642744274100
1.4159-1.43260.29622480.259542934293100
1.4326-1.450.26832240.246443404340100
1.45-1.46840.27442350.234542464246100
1.4684-1.48770.25782390.229443574357100
1.4877-1.50810.24352530.215542724272100
1.5081-1.52960.2172340.208843044304100
1.5296-1.55250.2222260.206443384338100
1.5525-1.57670.21922150.193842944294100
1.5767-1.60260.21232310.187343044304100
1.6026-1.63020.22622390.185643054305100
1.6302-1.65980.19062380.177342964296100
1.6598-1.69180.20292460.171742894289100
1.6918-1.72630.18172080.170543584358100
1.7263-1.76380.17022130.160243444344100
1.7638-1.80480.19312360.153243114311100
1.8048-1.850.16782330.151342974297100
1.85-1.90.1542300.155443044304100
1.9-1.95580.17352480.154843074307100
1.9558-2.0190.17282210.152143164316100
2.019-2.09110.15312120.1494336433699
2.0911-2.17480.16362200.153743564356100
2.1748-2.27370.16142330.15684276427699
2.2737-2.39350.16452700.15134279427999
2.3935-2.54340.1672190.15294296429699
2.5434-2.73960.1822150.1594317431799
2.7396-3.01490.17292190.16234348434899
3.0149-3.45040.16342110.15534348434899
3.4504-4.34410.14332500.14464353435399
4.3441-26.67920.16852140.15964431443199
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)
10.62770.06290.00710.6408-0.12910.8046-0.02140.08350.0297-0.06140.0350.0169-0.08070.0185-0.01770.0596-0.01070.00050.04990.00310.0298.0056.73858.7806
20.7336-0.02710.14220.76010.10080.54940.0225-0.0294-0.11920.06420.039-0.13910.04540.0768-0.05510.0610.0052-0.01710.062-0.0020.087220.85-5.63725.0197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A)
2X-RAY DIFFRACTION2(chain B)

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