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- PDB-4wzk: Crystal structure of P domain from norovirus strain Saga4 in comp... -

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Basic information

Entry
Database: PDB / ID: 4wzk
TitleCrystal structure of P domain from norovirus strain Saga4 in complex with HBGA type H2 (triglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid protein / Protruding domain
Function / homology
Function and homology information


virion component / host cell cytoplasm / metal ion 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
H type 2 antigen, alpha anomer / ACETATE ION / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII-4/Saga4/2006/JP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Derived calculations
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 / diffrn_radiation_wavelength / entity / entity_name_com / 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_molecule_features / 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.occupancy / _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_auth_seq_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_auth_seq_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 2.1Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2596
Polymers68,0822
Non-polymers1,1774
Water9,728540
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint1 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 58.810, 98.020
Angle α, β, γ (deg.)90.000, 108.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-747-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 222 - 530 / Label seq-ID: 1 - 309

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
Detailsbiological unit is the same as asym.

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Components

#1: Protein VP1


Mass: 34041.059 Da / Num. of mol.: 2 / Fragment: P DOMAIN (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII-4/Saga4/2006/JP / Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5BTR7
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / H type 2 antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 2 antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.47→46.58 Å / Num. obs: 102793 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 18.88 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.037 / Χ2: 1.048 / Net I/σ(I): 17.31 / Num. measured all: 302351
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.47-1.512.90.7880.482.2721685777874000.58195.1
1.51-1.550.8390.3892.921760755674150.47198.1
1.55-1.60.9140.2813.7420874736971980.34197.7
1.6-1.640.9380.2224.6219778714569770.27197.6
1.64-1.70.9650.176.121156698169130.20499
1.7-1.760.9750.1397.6320106668266050.16798.8
1.76-1.820.9840.1029.9918979646963730.12498.5
1.82-1.90.9880.08712.0217503627960910.10697
1.9-1.980.9930.06715.3616618597157880.08296.9
1.98-2.080.9950.05319.6517059574956540.06598.3
2.08-2.190.9960.04323.2816197544653540.05298.3
2.19-2.330.9970.03726.7914704514949970.04597
2.33-2.490.9980.03328.0712796486246970.0496.6
2.49-2.690.9980.0332.5813615455544750.03698.2
2.69-2.940.9980.02636.7112215417940630.03297.2
2.94-3.290.9990.02341.1710597376836080.02895.8
3.29-3.80.9990.02143.128653335531530.02694
3.8-4.650.9990.01847.488376284127290.02296.1
4.65-6.580.9990.01846.076188222421250.02295.5
6.580.9990.01946.553492125211780.02394.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.18 Å46.58 Å
Translation7.18 Å46.58 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOX

4oox


Resolution: 1.49→29.655 Å / FOM work R set: 0.9013 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1735 4958 5 %
Rwork0.1388 94240 -
obs0.1406 99198 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.74 Å2 / Biso mean: 25.46 Å2 / Biso min: 10.49 Å2
Refinement stepCycle: final / Resolution: 1.49→29.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 80 540 5407
Biso mean--47.94 33.08 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015031
X-RAY DIFFRACTIONf_angle_d1.2766881
X-RAY DIFFRACTIONf_chiral_restr0.056776
X-RAY DIFFRACTIONf_plane_restr0.007900
X-RAY DIFFRACTIONf_dihedral_angle_d12.5351831
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2848X-RAY DIFFRACTION3.624TORSIONAL
12B2848X-RAY DIFFRACTION3.624TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.50690.26411680.18983192336099
1.5069-1.52470.26361630.19273115327898
1.5247-1.54330.26181660.18513166333298
1.5433-1.56280.23411650.16473121328698
1.5628-1.58330.22951650.15593149331498
1.5833-1.6050.19111610.14653056321796
1.605-1.6280.2081650.14313129329497
1.628-1.65230.1941670.140431803347100
1.6523-1.67810.24181680.13743182335099
1.6781-1.70560.19531660.1373165333199
1.7056-1.7350.17171670.1333173334099
1.735-1.76650.18621650.12993133329899
1.7665-1.80050.16681680.12283187335598
1.8005-1.83730.18531660.1253145331198
1.8373-1.87720.18481640.12973132329697
1.8772-1.92090.17691580.13333011316994
1.9209-1.96890.16811670.12873172333999
1.9689-2.02210.15651680.11953198336699
2.0221-2.08160.17941660.12563151331798
2.0816-2.14880.15991670.12623164333198
2.1488-2.22550.1651650.12643150331598
2.2255-2.31460.16941630.12843090325397
2.3146-2.41990.16151640.13153120328497
2.4199-2.54740.18321650.13873138330397
2.5474-2.70690.17091670.14783168333598
2.7069-2.91580.17891670.15683163333097
2.9158-3.20890.17851630.14753106326996
3.2089-3.67250.16291610.14353065322694
3.6725-4.62410.14271660.12493142330896
4.6241-29.66040.17181670.14893177334495

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