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- PDB-4x06: Crystal structure of P domain from norovirus strain Saga4 in comp... -

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Basic information

Entry
Database: PDB / ID: 4x06
TitleCrystal structure of P domain from norovirus strain Saga4 in complex with HBGA type B (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
Biological speciesNorovirus Hu/GII-4/Saga4/2006/JP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.218 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / 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_alt_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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1776
Polymers68,0822
Non-polymers1,0954
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint7 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.830, 58.650, 97.310
Angle α, β, γ (deg.)90.000, 107.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21B-776-

HOH

31B-779-

HOH

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)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2-1/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}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.: 716 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
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: 0.97248 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97248 Å / Relative weight: 1
ReflectionHighest resolution: 1.22 Å / Num. obs: 176472 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.043 / Χ2: 1.006 / Net I/σ(I): 13.92 / Num. measured all: 457076
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.22-1.250.8380.3542.542930713462121480.44290.2
1.25-1.280.8810.3053.23334013079127670.37897.6
1.28-1.320.9020.2563.763207912704124560.31798
1.32-1.360.940.1964.622989312440121050.24597.3
1.36-1.410.9560.1675.623050611940116970.20798
1.41-1.460.9660.1396.893055511685114410.17297.9
1.46-1.510.9790.1118.482876711172109500.13898
1.51-1.570.9860.08810.162675810772104710.10997.2
1.57-1.640.990.0712.432554010375100700.08797.1
1.64-1.720.9930.05915.1126281992697050.07397.8
1.72-1.820.9950.04918.1424530937191770.06197.9
1.82-1.930.9960.04121.0322743894186580.05196.8
1.93-2.060.9970.03423.819952841780870.04396.1
2.06-2.220.9970.03227.2620488780275500.0496.8
2.22-2.440.9970.0328.9518676722369810.03796.6
2.44-2.720.9980.02829.7716134650262570.03596.2
2.72-3.150.9980.02631.4913913579855290.03395.4
3.15-3.850.9980.02634.4712885489747740.03297.5
3.85-5.450.9980.02834.049207381736090.03594.6
5.450.9960.03134.35522215520400.03994.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.2 Å48.1 Å
Translation7.2 Å48.1 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.5.3phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.218→32.323 Å / FOM work R set: 0.9212 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1612 8823 5 %
Rwork0.1341 167623 -
obs0.1354 176446 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.32 Å2 / Biso mean: 17.94 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.218→32.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 140 716 5617
Biso mean--27.73 26.24 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095184
X-RAY DIFFRACTIONf_angle_d1.3577102
X-RAY DIFFRACTIONf_chiral_restr0.087777
X-RAY DIFFRACTIONf_plane_restr0.008925
X-RAY DIFFRACTIONf_dihedral_angle_d12.5072004
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 (%)
1.2182-1.2320.22652480.18484703495182
1.232-1.24650.22322920.17185557584997
1.2465-1.26170.222950.16135602589797
1.2617-1.27770.20832960.15645620591698
1.2777-1.29450.18672950.15575603589898
1.2945-1.31220.20812990.15795680597998
1.3122-1.3310.21022970.14755643594098
1.331-1.35080.19132940.13375596589098
1.3508-1.37190.18042920.13265539583197
1.3719-1.39440.19262990.12945683598298
1.3944-1.41850.17132950.12455619591498
1.4185-1.44430.16622980.12215647594598
1.4443-1.47210.14582970.11715656595398
1.4721-1.50210.15512980.11455656595498
1.5021-1.53480.15962960.11315622591898
1.5348-1.57050.16592930.11235563585697
1.5705-1.60970.15792930.11325564585796
1.6097-1.65330.1622980.11025664596298
1.6533-1.70190.16022950.11485612590798
1.7019-1.75680.15762980.11565658595698
1.7568-1.81960.14552980.11475660595898
1.8196-1.89250.15572970.12125638593597
1.8925-1.97860.16472910.12475538582996
1.9786-2.08290.14722940.12155579587396
2.0829-2.21340.13952950.12445618591397
2.2134-2.38420.152960.1245623591997
2.3842-2.6240.152950.13635606590197
2.624-3.00350.16382900.14815509579995
3.0035-3.78320.1523010.14015712601397
3.7832-32.33450.16752980.1575653595195

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