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- PDB-3ry8: Structural basis for norovirus inhibition and fucose mimicry by c... -

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Basic information

Entry
Database: PDB / ID: 3ry8
TitleStructural basis for norovirus inhibition and fucose mimicry by citrate
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN
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
CITRATE ANION / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHansman, G.S. / McLellan, J.S. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2012
Title: Structural basis for norovirus inhibition and fucose mimicry by citrate.
Authors: Hansman, G.S. / Shahzad-Ul-Hussan, S. / McLellan, J.S. / Chuang, G.Y. / Georgiev, I. / Shimoike, T. / Katayama, K. / Bewley, C.A. / Kwong, P.D.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 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)70,48214
Polymers69,6102
Non-polymers87212
Water14,556808
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint19 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.763, 79.811, 69.605
Angle α, β, γ (deg.)90.00, 96.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein / Capsid


Mass: 34804.953 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) / Strain (production host): BL21(DE3) / References: UniProt: Q5F4T5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium citrate (0.66 M) and isopropanol (1.65% v/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR225 CCD / Detector: CCD / Date: Sep 10, 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: 136131 / Num. obs: 136131 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.15 / Num. unique all: 13552 / % possible all: 99.6

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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: 1.4→31.975 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1506 6674 -RANDOM
Rwork0.1388 ---
all0.1394 131576 --
obs0.1394 131576 96.56 %-
Refinement stepCycle: LAST / Resolution: 1.4→31.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 57 808 5587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_df_plane_restr0.009
X-RAY DIFFRACTIONf_chiral_restr0.088
X-RAY DIFFRACTIONf_dihedral_angle_d12.433
X-RAY DIFFRACTIONf_angle_d1.393
X-RAY DIFFRACTIONf_bond_d0.011

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