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- PDB-3q6q: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 0... -

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Basic information

Entry
Database: PDB / ID: 3q6q
TitleCrystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with disordered HBGA type Lea
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: 1.43 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
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)70,87922
Polymers69,6102
Non-polymers1,26920
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-14 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.150, 78.962, 69.243
Angle α, β, γ (deg.)90.00, 99.67, 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.: 16 / 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.: 753 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
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: 1.43→28.971 Å / Num. all: 123161 / Num. obs: 123161 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.83 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.039 / Net I/σ(I): 22.04
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.16 / Num. unique all: 8862 / Rsym value: 0.653 / % possible all: 94.1

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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: 1.43→28.971 Å / SU ML: 0.18 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 6168 5.01 %RANDOM
Rwork0.1773 ---
obs0.1778 123157 96.63 %-
all-123157 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.263 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 21.768 Å2
Baniso -1Baniso -2Baniso -3
1--1.0584 Å20 Å2-1.47 Å2
2---1.8628 Å20 Å2
3---2.9211 Å2
Refinement stepCycle: LAST / Resolution: 1.43→28.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 84 753 5666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055091
X-RAY DIFFRACTIONf_angle_d0.9846936
X-RAY DIFFRACTIONf_dihedral_angle_d12.0041823
X-RAY DIFFRACTIONf_chiral_restr0.067766
X-RAY DIFFRACTIONf_plane_restr0.005918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.43-1.44630.32971720.32473823382394
1.4463-1.46330.31092160.29353778377895
1.4633-1.48110.31252190.27193789378995
1.4811-1.49990.28292170.25763770377095
1.4999-1.51960.25062060.25023840384095
1.5196-1.54040.24872000.23583820382095
1.5404-1.56240.24711950.22323821382195
1.5624-1.58570.21761870.21333880388095
1.5857-1.61050.26392150.21613847384796
1.6105-1.63690.27312150.21443802380295
1.6369-1.66510.21562190.21163862386296
1.6651-1.69540.23952170.20473859385996
1.6954-1.7280.19771800.19183917391796
1.728-1.76330.1972010.18613835383596
1.7633-1.80160.21322140.1723920392097
1.8016-1.84350.16382050.16743847384797
1.8435-1.88960.16862040.16973919391997
1.8896-1.94070.19832320.17023894389497
1.9407-1.99780.17511990.16733901390197
1.9978-2.06230.17811980.17073958395897
2.0623-2.13590.18581810.16853976397698
2.1359-2.22140.17552110.17263925392598
2.2214-2.32250.15892230.1673975397598
2.3225-2.44490.18192160.16173935393598
2.4449-2.5980.16971990.16773955395598
2.598-2.79840.18612150.17453985398598
2.7984-3.07970.1881950.17244002400298
3.0797-3.52470.17681900.16414012401298
3.5247-4.43820.14782240.14714022402299
4.4382-28.97650.17712030.16944120412099
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)
10.15630.04770.14990.08140.01190.165-0.0040.05720.0178-0.02970.01460.0213-0.09070.0616-0.01550.0551-0.00170.00760.0227-0.00820.0028.39927.55610.1152
20.13910.0012-0.11410.1583-0.03540.38870.023-0.01580.05520.06730.04160.0159-0.1342-0.0145-0.04340.10380.00690.00210.05390.0010.06373.858513.619319.3391
30.0352-0.00790.00880.1469-0.01880.0064-0.00690.0656-0.0338-0.13490.03650.01590.00490.0256-0.00920.084-0.01880.03060.0974-0.0387-0.023712.8438-2.0562-4.3308
40.14140.06340.14630.13090.05210.15750.02980.0443-0.05260.03680.0123-0.07620.02650.0473-0.0365-0.0040.0001-0.01670.0144-0.00640.051120.2378-5.771523.6592
50.40090.05510.11320.0237-0.01320.14190.0237-0.0232-0.17980.00890.02390.00340.0887-0.0271-0.06110.02170.0115-0.0333-0.03290.03760.04919.4102-12.462827.4506
60.09190.08370.16460.48780.11950.29680.02060.1176-0.12050.02130.0438-0.2772-0.01390.0759-0.064-0.011-0.0045-0.00860.0702-0.04610.124833.88082.471922.5837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 224:307)
2X-RAY DIFFRACTION2(chain A and resid 308:432)
3X-RAY DIFFRACTION3(chain A and resid 433:538)
4X-RAY DIFFRACTION4(chain B and resid 224:300)
5X-RAY DIFFRACTION5(chain B and resid 301:434)
6X-RAY DIFFRACTION6(chain B and resid 435:538)

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