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- PDB-9edq: GX/NPIH26 bat norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 9edq
TitleGX/NPIH26 bat 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 speciesBat norovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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)64,9616
Polymers64,5762
Non-polymers3844
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-70 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.490, 67.490, 238.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein VP1


Mass: 32288.195 Da / Num. of mol.: 2 / Fragment: protruding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat norovirus / Strain: GX/NPIH26 / Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S1TZT6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.6 M magnesium sulfate heptahydrate, 0.1 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.63→47.75 Å / Num. obs: 79732 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.041 / Rrim(I) all: 0.151 / Χ2: 0.57 / Net I/σ(I): 11.1 / Num. measured all: 1071388
Reflection shellResolution: 1.63→1.66 Å / % possible obs: 97.5 % / Redundancy: 13.1 % / Rmerge(I) obs: 1.654 / Num. measured all: 49582 / Num. unique obs: 3791 / CC1/2: 0.639 / Rpim(I) all: 0.467 / Rrim(I) all: 1.721 / Χ2: 0.52 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→47.11 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 3975 5 %
Rwork0.1624 --
obs0.1639 79483 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 20 862 5421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064959
X-RAY DIFFRACTIONf_angle_d0.7966838
X-RAY DIFFRACTIONf_dihedral_angle_d11.1481762
X-RAY DIFFRACTIONf_chiral_restr0.057749
X-RAY DIFFRACTIONf_plane_restr0.007917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.23251370.24212610X-RAY DIFFRACTION98
1.65-1.670.28021390.24862635X-RAY DIFFRACTION100
1.67-1.70.28721410.23012671X-RAY DIFFRACTION100
1.7-1.720.27261400.22672666X-RAY DIFFRACTION100
1.72-1.740.24591390.21682636X-RAY DIFFRACTION100
1.74-1.770.24571420.20212705X-RAY DIFFRACTION100
1.77-1.80.22931380.18772628X-RAY DIFFRACTION100
1.8-1.830.24491430.18242701X-RAY DIFFRACTION100
1.83-1.860.1981380.17532631X-RAY DIFFRACTION100
1.86-1.890.23841400.1842663X-RAY DIFFRACTION100
1.89-1.930.22211420.18432687X-RAY DIFFRACTION100
1.93-1.970.22911400.18392666X-RAY DIFFRACTION100
1.97-2.010.18311400.17162651X-RAY DIFFRACTION100
2.01-2.060.21271410.15362683X-RAY DIFFRACTION100
2.06-2.110.21731430.15912715X-RAY DIFFRACTION100
2.11-2.170.19641400.15322667X-RAY DIFFRACTION100
2.17-2.230.19531410.15852677X-RAY DIFFRACTION100
2.23-2.30.19311400.15412668X-RAY DIFFRACTION100
2.3-2.380.18491440.15662734X-RAY DIFFRACTION100
2.38-2.480.20261420.15822685X-RAY DIFFRACTION100
2.48-2.590.20951430.16022721X-RAY DIFFRACTION100
2.59-2.730.21221410.16712679X-RAY DIFFRACTION100
2.73-2.90.18521430.16142714X-RAY DIFFRACTION100
2.9-3.120.16081440.16552748X-RAY DIFFRACTION100
3.12-3.440.1941450.15022749X-RAY DIFFRACTION100
3.44-3.930.1751440.13342760X-RAY DIFFRACTION100
3.93-4.960.12321480.12462808X-RAY DIFFRACTION100
4.96-47.110.19741570.17322950X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.6964 Å / Origin y: -25.255 Å / Origin z: 20.1292 Å
111213212223313233
T0.0849 Å2-0.0144 Å2-0.0116 Å2-0.126 Å20.0018 Å2--0.085 Å2
L0.491 °20.0022 °2-0.1458 °2-0.5303 °2-0.1421 °2--0.6984 °2
S0.0207 Å °-0.0036 Å °-0.0093 Å °-0.0128 Å °0.0139 Å °0.0296 Å °0.0111 Å °-0.0311 Å °-0.0273 Å °
Refinement TLS groupSelection details: all

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