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- PDB-9edm: GII.9-VA97207 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 9edm
TitleGII.9-VA97207 norovirus protruding domain
ComponentsCapsid
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 / Capsid
Function and homology information
Biological speciesHuman calicivirus NLV/VA97207/1997
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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: Capsid
B: Capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6414
Polymers66,5702
Non-polymers712
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.190, 96.890, 65.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Capsid


Mass: 33285.086 Da / Num. of mol.: 2 / Fragment: protruding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human calicivirus NLV/VA97207/1997 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q91H09
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 7.0), 30% v/v Jeffamine ED-2003

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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: Oct 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.98→48.44 Å / Num. obs: 42579 / % possible obs: 99.3 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.071 / Rrim(I) all: 0.241 / Χ2: 0.57 / Net I/σ(I): 8.5
Reflection shellResolution: 1.98→2.02 Å / % possible obs: 94.5 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.791 / Num. measured all: 30735 / Num. unique obs: 2810 / CC1/2: 0.54 / Rpim(I) all: 0.554 / Rrim(I) all: 1.877 / Χ2: 0.54 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER9.0.002phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→47.13 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 2121 5 %
Rwork0.1645 --
obs0.1668 42414 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 2 557 5249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064864
X-RAY DIFFRACTIONf_angle_d0.836640
X-RAY DIFFRACTIONf_dihedral_angle_d13.0511769
X-RAY DIFFRACTIONf_chiral_restr0.054715
X-RAY DIFFRACTIONf_plane_restr0.008896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.30411370.25432592X-RAY DIFFRACTION98
2.03-2.080.25631390.23312634X-RAY DIFFRACTION99
2.08-2.130.26251390.21892652X-RAY DIFFRACTION99
2.13-2.20.2521400.2132647X-RAY DIFFRACTION99
2.2-2.270.2821380.20832628X-RAY DIFFRACTION99
2.27-2.350.2231410.1882678X-RAY DIFFRACTION99
2.35-2.440.24231390.18982651X-RAY DIFFRACTION99
2.44-2.550.24961410.17982677X-RAY DIFFRACTION99
2.55-2.690.24881400.17772662X-RAY DIFFRACTION100
2.69-2.850.24741420.18212687X-RAY DIFFRACTION100
2.85-3.080.24471410.17072682X-RAY DIFFRACTION100
3.08-3.380.22811420.15692706X-RAY DIFFRACTION100
3.38-3.870.171450.13662745X-RAY DIFFRACTION100
3.87-4.880.14611450.11752758X-RAY DIFFRACTION100
4.88-47.130.16081520.1412894X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.9054 Å / Origin y: 25.9249 Å / Origin z: -15.5366 Å
111213212223313233
T0.186 Å20.0025 Å2-0.0072 Å2-0.1928 Å2-0.0014 Å2--0.1743 Å2
L0.4597 °2-0.2058 °2-0.018 °2-0.7523 °20.0947 °2--0.4174 °2
S-0.0396 Å °-0.0271 Å °0.0114 Å °0.0859 Å °0.0468 Å °0.014 Å °0.0282 Å °0.0055 Å °-0.0067 Å °
Refinement TLS groupSelection details: all

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