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Basic information

Entry
Database: PDB / ID: 2zl6
TitleAtomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus
Components58 kd capsid protein
KeywordsVIRAL PROTEIN / Norovirus / Norwalk virus / HBGA / histo-blood group antigen / carbohydrate / VP1 / P-domain
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
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
ACETATE ION / Capsid protein VP1
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsChoi, J.M. / Huston, A.M. / Estes, M.K. / Prasad, B.V.V.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus
Authors: Choi, J.M. / Hutson, A.M. / Estes, M.K. / Prasad, B.V.V.
History
DepositionApr 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: 58 kd capsid protein
B: 58 kd capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0206
Polymers63,0592
Non-polymers9614
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-0.2 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.512, 83.512, 162.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-835-

HOH

21B-888-

HOH

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Components

#1: Protein 58 kd capsid protein


Mass: 31529.301 Da / Num. of mol.: 2 / Fragment: P-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Strain: G.I / Gene: ORF2 / Plasmid: pHisMal-C2ET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83884
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 853.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2-4/a4-b1_b3-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M Citric Acid(pH 3.8), 0.2M Ammonium Nitrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2007
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.43→41.73 Å / Num. all: 121668 / Num. obs: 121303 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.38 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ihm

1ihm


Resolution: 1.43→40.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.075 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20048 5880 5 %RANDOM
Rwork0.17915 ---
obs0.18023 110616 95.51 %-
all-115816 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.43→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 64 823 5208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224561
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9786275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14624.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89115623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4231512
X-RAY DIFFRACTIONr_chiral_restr0.090.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023547
X-RAY DIFFRACTIONr_nbd_refined0.2050.22225
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2632
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.255
X-RAY DIFFRACTIONr_mcbond_it0.8131.52932
X-RAY DIFFRACTIONr_mcangle_it1.38524711
X-RAY DIFFRACTIONr_scbond_it1.83131813
X-RAY DIFFRACTIONr_scangle_it2.564.51557
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 298 -
Rwork0.261 5310 -
obs--62.74 %

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