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

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Basic information

Entry
Database: PDB / ID: 3ony
TitleCrystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with Fucose
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / capsid protein
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
alpha-L-fucopyranose / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,26716
Polymers104,1543
Non-polymers1,11313
Water13,097727
1
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,19911
Polymers69,4362
Non-polymers7639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Capsid protein
hetero molecules

C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,13610
Polymers69,4362
Non-polymers7018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
3
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0685
Polymers34,7181
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1306
Polymers34,7181
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0685
Polymers34,7181
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.529, 115.905, 267.801
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
11C-107-

HOH

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Components

#1: Protein Capsid protein


Mass: 34717.879 Da / Num. of mol.: 3 / 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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.66M ammonium citrate pH 6.5, 1.65% isopropanol, 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: Apr 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: 1.85→50 Å / Num. all: 105679 / Num. obs: 105679 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 %
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.2 / % possible all: 93.3

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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
Starting model: PDB ID: 3ONU

3onu


Resolution: 1.85→25.666 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 5035 5.04 %
Rwork0.164 --
obs0.1652 99983 93.65 %
all-99983 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.465 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6314 Å20 Å2-0 Å2
2--6.0657 Å2-0 Å2
3----7.6971 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7149 0 73 727 7949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077419
X-RAY DIFFRACTIONf_angle_d1.04110150
X-RAY DIFFRACTIONf_dihedral_angle_d11.322658
X-RAY DIFFRACTIONf_chiral_restr0.2421144
X-RAY DIFFRACTIONf_plane_restr0.0051333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8504-1.87150.31781220.27242167X-RAY DIFFRACTION64
1.8715-1.89350.32641170.27972260X-RAY DIFFRACTION69
1.8935-1.91660.29661550.25232899X-RAY DIFFRACTION85
1.9166-1.94080.25251540.23633082X-RAY DIFFRACTION93
1.9408-1.96630.23451440.20792805X-RAY DIFFRACTION83
1.9663-1.99330.21061400.1912920X-RAY DIFFRACTION88
1.9933-2.02170.20761600.1743034X-RAY DIFFRACTION90
2.0217-2.05190.1931550.1713161X-RAY DIFFRACTION95
2.0519-2.08390.20941640.17423205X-RAY DIFFRACTION95
2.0839-2.11810.19561830.17383146X-RAY DIFFRACTION95
2.1181-2.15460.2341940.16213141X-RAY DIFFRACTION95
2.1546-2.19380.22551900.17223124X-RAY DIFFRACTION93
2.1938-2.23590.2141770.18163068X-RAY DIFFRACTION92
2.2359-2.28150.22722030.19553282X-RAY DIFFRACTION99
2.2815-2.33110.20451670.1713047X-RAY DIFFRACTION91
2.3311-2.38530.19141570.15273250X-RAY DIFFRACTION96
2.3853-2.44490.20741850.16163269X-RAY DIFFRACTION97
2.4449-2.5110.18571740.15073302X-RAY DIFFRACTION98
2.511-2.58480.1821730.15313285X-RAY DIFFRACTION98
2.5848-2.66810.18161710.15393302X-RAY DIFFRACTION98
2.6681-2.76340.19281900.16323335X-RAY DIFFRACTION99
2.7634-2.87390.16581400.16933394X-RAY DIFFRACTION99
2.8739-3.00450.1971650.1633350X-RAY DIFFRACTION99
3.0045-3.16260.18591830.1633376X-RAY DIFFRACTION100
3.1626-3.36040.20541580.173470X-RAY DIFFRACTION100
3.3604-3.61920.18931710.16813361X-RAY DIFFRACTION100
3.6192-3.98220.15642100.14873391X-RAY DIFFRACTION100
3.9822-4.55560.1411870.12093435X-RAY DIFFRACTION100
4.5556-5.72910.15631820.13353475X-RAY DIFFRACTION100
5.7291-25.66840.20221640.18613612X-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)
11.07840.08550.04650.7703-0.46431.93130.22730.096-0.0236-0.0716-0.04760.02830.1026-0.2071-0.16730.16610.019-0.02530.15970.0070.1571-3.210234.1024-32.7839
21.65160.06990.27630.745-0.56732.31670.2641-0.456-0.09060.2228-0.1012-0.0054-0.04930.257-0.13310.2076-0.0728-0.0420.23570.0360.12365.969531.1466-11.5369
31.1883-0.1915-0.81180.7926-0.32131.98940.115-0.19250.02890.11690.05730.0662-0.1945-0.0184-0.15630.12880.00630.03160.1292-0.00290.157636.119333.3754-56.0259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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