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- PDB-9olu: GX/NPIH26 bat norovirus protruding domain in complex with L-fucose -

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Basic information

Entry
Database: PDB / ID: 9olu
TitleGX/NPIH26 bat norovirus protruding domain in complex with L-fucose
ComponentsVP1
KeywordsVIRAL PROTEIN / norovirus / P domain
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
alpha-L-fucopyranose / VP1
Similarity search - Component
Biological speciesBat norovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHolroyd, D.L. / Bruning, J.B. / Hansman, G.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: GX/NPIH26 bat norovirus protruding domain in complex with L-fucose
Authors: Holroyd, D.L. / Bruning, J.B. / Hansman, G.S.
History
DepositionMay 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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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)64,9054
Polymers64,5762
Non-polymers3282
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-5 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.542, 67.542, 238.385
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: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.57 %
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: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.55→47.68 Å / Num. obs: 91925 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Χ2: 0.54 / Net I/σ(I): 16.5 / Num. measured all: 1225877
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 95.3 % / Redundancy: 12.5 % / Rmerge(I) obs: 1.417 / Num. measured all: 54189 / Num. unique obs: 4332 / CC1/2: 0.643 / Rpim(I) all: 0.407 / Rrim(I) all: 1.477 / Χ2: 0.46 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→36.96 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 1992 2.17 %
Rwork0.158 --
obs0.1588 91803 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 22 792 5376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144912
X-RAY DIFFRACTIONf_angle_d1.2536781
X-RAY DIFFRACTIONf_dihedral_angle_d11.5141803
X-RAY DIFFRACTIONf_chiral_restr0.087762
X-RAY DIFFRACTIONf_plane_restr0.013901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.36451400.30436149X-RAY DIFFRACTION97
1.59-1.640.34211410.27176345X-RAY DIFFRACTION100
1.64-1.680.25041390.22036342X-RAY DIFFRACTION100
1.68-1.740.23071400.18856354X-RAY DIFFRACTION100
1.74-1.80.21131420.1776319X-RAY DIFFRACTION100
1.8-1.870.20981430.16346398X-RAY DIFFRACTION100
1.87-1.960.20361410.1866334X-RAY DIFFRACTION100
1.96-2.060.20581440.15556398X-RAY DIFFRACTION100
2.06-2.190.19511400.1596407X-RAY DIFFRACTION100
2.19-2.360.16041390.14816413X-RAY DIFFRACTION100
2.36-2.60.18881430.16786479X-RAY DIFFRACTION100
2.6-2.970.21691450.15976474X-RAY DIFFRACTION100
2.97-3.750.17551450.14986568X-RAY DIFFRACTION100
3.75-36.960.16791500.13076831X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.8996 Å / Origin y: -33.2441 Å / Origin z: 19.6436 Å
111213212223313233
T0.1447 Å2-0.0334 Å2-0.0059 Å2-0.1539 Å20.0042 Å2--0.1205 Å2
L0.9473 °2-0.0304 °20.4464 °2-1.1112 °20.0136 °2--1.0266 °2
S0.0381 Å °-0.0516 Å °-0.0367 Å °0.0128 Å °0.086 Å °-0.0071 Å °0.0624 Å °-0.0475 Å °-0.0972 Å °
Refinement TLS groupSelection details: all

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