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

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Basic information

Entry
Database: PDB / ID: 4wzl
TitleCrystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Lea (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
Lewis A 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: 1.7 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / 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.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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_molecule_features / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)69,73417
Polymers67,8802
Non-polymers1,85415
Water10,215567
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint31 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.870, 58.830, 124.440
Angle α, β, γ (deg.)90.000, 119.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21B-759-

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: GLY / Beg label comp-ID: GLY / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 223 - 530 / Label seq-ID: 1 - 308

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: 33939.953 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 beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis A antigen, alpha anomer
DescriptorTypeProgram
DGalpb1-3[LFucpa1-4]DGlcpNAca1-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/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
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: 1.57→49.59 Å / Num. obs: 82519 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.063 / Χ2: 1.074 / Net I/σ(I): 8.11 / Num. measured all: 246067
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
1.57-1.610.9070.4871.9915906619854910.59188.6
1.61-1.660.930.4052.417811606259730.4998.5
1.66-1.710.9580.3222.8216667592557700.39197.4
1.71-1.760.9670.2743.3516189570455440.33297.2
1.76-1.820.9790.2064.3916961556955230.24799.2
1.82-1.880.9840.184.9516178538953290.21798.9
1.88-1.950.9890.1435.9115374521751350.17398.4
1.95-2.030.9940.1067.1114356502548950.12997.4
2.03-2.120.9950.0858.3113485476946400.10397.3
2.12-2.220.9960.0779.3814039457045420.09399.4
2.22-2.340.9970.06410.3313308439443490.07799
2.34-2.490.9970.05910.9912347412340700.07298.7
2.49-2.660.9970.05311.6510728391338060.06597.3
2.66-2.870.9980.04613.2211198364035930.05698.7
2.87-3.140.9990.03715.0510317336433250.04598.8
3.14-3.520.9980.03316.348976301729720.0498.5
3.52-4.060.9990.02916.567236270226170.03596.9
4.06-4.970.9990.02618.146952226222110.03297.7
4.97-7.030.9990.02717.675200179817570.03397.7
7.030.9990.02518.1283910159770.0396.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å49.59 Å
Translation2.5 Å49.59 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.4.0phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.467 Å / FOM work R set: 0.6267 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 38.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 3280 4.99 %
Rwork0.1703 62422 -
obs0.1715 65702 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.26 Å2 / Biso mean: 18.75 Å2 / Biso min: 3.78 Å2
Refinement stepCycle: final / Resolution: 1.7→42.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 124 569 5475
Biso mean--37.42 28.24 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055077
X-RAY DIFFRACTIONf_angle_d1.0486926
X-RAY DIFFRACTIONf_chiral_restr0.039774
X-RAY DIFFRACTIONf_plane_restr0.005906
X-RAY DIFFRACTIONf_dihedral_angle_d12.7731849
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2906X-RAY DIFFRACTION0.34TORSIONAL
12B2906X-RAY DIFFRACTION0.34TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72540.30971410.26662674281596
1.7254-1.75240.30781390.25612657279698
1.7524-1.78110.25621440.24132751289599
1.7811-1.81180.22891430.22152715285899
1.8118-1.84470.23581430.21552712285599
1.8447-1.88020.24881440.21292738288299
1.8802-1.91860.24991410.19992696283799
1.9186-1.96030.23341430.19332728287198
1.9603-2.00590.19541410.18182670281198
2.0059-2.05610.18931370.17992656279396
2.0561-2.11170.20771430.1752715285898
2.1117-2.17380.19421440.17462745288999
2.1738-2.2440.18551430.16052717286099
2.244-2.32420.18671440.15852721286599
2.3242-2.41720.19221430.15242742288599
2.4172-2.52720.17251430.15992706284998
2.5272-2.66040.25841420.15922706284897
2.6604-2.82710.17451450.16262745289099
2.8271-3.04530.15921440.15532761290599
3.0453-3.35170.16941440.14832739288399
3.3517-3.83640.15021430.1442713285698
3.8364-4.83230.17471440.13522740288498
4.8323-42.48040.20281420.18422675281793
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)
10.7121-0.11520.10670.0999-0.08560.29020.0496-0.2358-0.13590.0920.01390.00610.0076-0.02970.20160.11820.03650.02190.15670.01140.0501179.4605-26.589437.4176
20.3799-0.15650.10080.6131-0.23910.60020.047-0.24650.21530.2150.11820.3489-0.4811-0.05250.28230.17380-0.01390.1001-0.09350.0488170.1168-8.563336.215
30.5794-0.0233-0.12520.0795-0.0440.3506-0.0242-0.4418-0.13750.16610.0337-0.01150.10640.11380.05560.16920.0248-0.03890.21240.06050.113184.6247-29.408242.195
40.31610.1423-0.23470.28210.01210.29090.08-0.2321-0.12260.1770.0179-0.15460.08380.09570.110.15060.03390.00280.16530.07080.1945193.8272-38.264941.5093
50.16810.01820.15980.1261-0.00310.17030.1294-0.0411-0.27640.0211-0.01480.00560.27990.01170.23960.14820.0295-0.0504-0.1025-0.06550.164172.482-31.901621.5781
60.5576-0.06990.00720.2174-0.01-0.00270.04410.4228-0.0121-0.20970.01190.0003-0.0048-0.20860.05290.11580.0096-0.04390.1516-0.02970.0845171.2905-25.74977.7113
70.0611-0.0435-0.02420.1603-0.18150.3053-0.03190.01120.04560.0569-0.0874-0.1159-0.13970.1435-0.1680.04650.0024-0.0246-0.1107-0.05630.1458186.0269-21.79517.9477
80.0414-0.01570.0350.23510.08540.1292-0.00180.0404-0.03930.02210.0577-0.262-0.08530.13170.03170.1219-0.0220.0695-0.0949-0.04080.2296192.7264-13.717715.4944
90.0327-0.0041-0.02850.13270.03480.02880.0237-0.11280.1581-0.0505-0.0616-0.0368-0.12670.07540.01520.1199-0.07080.0155-0.0113-0.06340.1056185.0962-7.272222.5627
100.27170.130.03010.2216-0.0520.6094-0.00750.13250.2735-0.13880.03950.0211-0.4137-0.0879-0.01220.1193-0.08530.0266-0.07550.00370.1673183.1398-5.970916.3628
110.168-0.0280.07540.11540.06390.0938-0.05570.13460.0583-0.1473-0.0129-0.1273-0.0707-0.0198-0.0840.10440.01810.06090.09090.03110.0713182.4262-17.1193.7327
120.2453-0.10070.00580.24140.18330.53180.02490.1277-0.0266-0.1431-0.0146-0.0277-0.1434-0.2128-0.1370.01230.04640.03060.0001-0.02750.0671171.2653-26.488813.8291
130.06480.05550.11510.0890.05240.26160.1501-0.0168-0.07250.10390.0044-0.0830.19710.03170.31760.1052-0.0206-0.00090.0961-0.06040.273167.291-43.020616.5518
140.14550.0841-0.0130.0759-0.04660.06790.03460.0224-0.07250.01360.010.19230.0885-0.03990.0975-0.1423-0.1109-0.03160.0875-0.10710.1993165.4971-38.145611.3482
150.12010.00930.01360.07750.02820.0903-0.03020.2572-0.1719-0.10360.02310.1010.0818-0.08690.04690.1317-0.0249-0.05280.2508-0.04650.2118162.7303-38.26612.4819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 292 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 293 through 399 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 500 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 501 through 530 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 223 through 247 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 248 through 266 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 267 through 292 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 293 through 323 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 324 through 352 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 353 through 399 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 400 through 419 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 420 through 464 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 465 through 483 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 484 through 500 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 501 through 530 )B0

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