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- PDB-9edo: GII.27: Loreto0959 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 9edo
TitleGII.27: Loreto0959 norovirus protruding domain
ComponentsVP1
KeywordsVIRAL PROTEIN / norovirus / P domain
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1
Function and homology information
Biological speciesNorovirus GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsHolroyd, D.L. / Kumar, A. / Bruning, J.B. / Hansman, G.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2025
Title: Antigenic structural analysis of bat and human norovirus protruding (P) domains.
Authors: Holroyd, D.L. / Kumar, A. / Vasquez, E. / Masic, V. / von Itzstein, M. / Bruning, J.B. / Hansman, G.S.
History
DepositionNov 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)68,7023
Polymers68,6662
Non-polymers351
Water16,772931
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-19 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.150, 90.560, 67.120
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VP1


Mass: 34333.137 Da / Num. of mol.: 2 / Fragment: P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4Y8Z8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.17 M ammonium sulfate, 25.5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.42→49.09 Å / Num. obs: 109595 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Χ2: 0.49 / Net I/σ(I): 9.7 / Num. measured all: 623429
Reflection shellResolution: 1.42→1.44 Å / % possible obs: 88 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.695 / Num. measured all: 26748 / Num. unique obs: 4837 / CC1/2: 0.861 / Rpim(I) all: 0.311 / Rrim(I) all: 0.763 / Χ2: 0.33 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→49.08 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1746 5479 5 %
Rwork0.1334 --
obs0.1354 109563 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4791 0 1 931 5723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055217
X-RAY DIFFRACTIONf_angle_d0.7747179
X-RAY DIFFRACTIONf_dihedral_angle_d11.7741937
X-RAY DIFFRACTIONf_chiral_restr0.08761
X-RAY DIFFRACTIONf_plane_restr0.008973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.25911570.19232970X-RAY DIFFRACTION86
1.44-1.450.19381830.17533492X-RAY DIFFRACTION100
1.45-1.470.20771830.15893469X-RAY DIFFRACTION100
1.47-1.490.20821820.15753463X-RAY DIFFRACTION100
1.49-1.510.18721840.15133496X-RAY DIFFRACTION100
1.51-1.530.20351820.15483460X-RAY DIFFRACTION100
1.53-1.550.21691840.15813482X-RAY DIFFRACTION100
1.55-1.580.18511810.14693454X-RAY DIFFRACTION100
1.58-1.60.20331870.1463546X-RAY DIFFRACTION100
1.6-1.630.20021800.14473427X-RAY DIFFRACTION100
1.63-1.650.18431830.13443465X-RAY DIFFRACTION100
1.65-1.690.17381840.12913495X-RAY DIFFRACTION100
1.69-1.720.17571820.12793459X-RAY DIFFRACTION100
1.72-1.750.17781840.12323502X-RAY DIFFRACTION100
1.75-1.790.14581820.12553461X-RAY DIFFRACTION100
1.79-1.830.18051840.13153486X-RAY DIFFRACTION100
1.83-1.880.18581830.13923484X-RAY DIFFRACTION100
1.88-1.930.18521840.14273499X-RAY DIFFRACTION100
1.93-1.990.15741830.13333471X-RAY DIFFRACTION100
1.99-2.050.16371850.13213506X-RAY DIFFRACTION100
2.05-2.120.16841820.13433471X-RAY DIFFRACTION100
2.12-2.210.16731840.13213482X-RAY DIFFRACTION100
2.21-2.310.18751830.13843481X-RAY DIFFRACTION100
2.31-2.430.17221830.13953481X-RAY DIFFRACTION100
2.43-2.580.20261850.14773523X-RAY DIFFRACTION100
2.58-2.780.17171830.14633463X-RAY DIFFRACTION100
2.78-3.060.18771840.13853504X-RAY DIFFRACTION100
3.06-3.50.17911850.12393510X-RAY DIFFRACTION100
3.5-4.410.13691840.10593504X-RAY DIFFRACTION100
4.42-49.080.16931890.1263578X-RAY DIFFRACTION100

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