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- PDB-9olt: GII.27: Loreto0959 norovirus protruding domain complexed with A-t... -

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Basic information

Entry
Database: PDB / ID: 9olt
TitleGII.27: Loreto0959 norovirus protruding domain complexed with A-trisaccharide
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: 1.76 Å
AuthorsHolroyd, D.L. / Bruning, J.B. / Hansman, G.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: GII.27: Loreto0959 Human norovirus protruding domain in complex with A-trisaccharide
Authors: Holroyd, D.L. / Bruning, J.B. / Hansman, G.S.
History
DepositionMay 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 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)69,61211
Polymers68,6662
Non-polymers9469
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-1 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.939, 90.695, 66.786
Angle α, β, γ (deg.)90.00, 106.04, 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
Details: SER 224 is leftover from the expression tag / Source: (gene. exp.) Norovirus GII / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4Y8Z8
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
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: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.76→45.45 Å / Num. obs: 57076 / % possible obs: 99 % / Redundancy: 8.2 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.022 / Rrim(I) all: 0.064 / Χ2: 0.53 / Net I/σ(I): 16.8 / Num. measured all: 469281
Reflection shellResolution: 1.76→1.8 Å / % possible obs: 94.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.533 / Num. measured all: 24899 / Num. unique obs: 3058 / CC1/2: 0.91 / Rpim(I) all: 0.194 / Rrim(I) all: 0.568 / Χ2: 0.47 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→45.45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 2000 3.51 %
Rwork0.1486 --
obs0.1503 57043 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 59 708 5596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085128
X-RAY DIFFRACTIONf_angle_d0.9457024
X-RAY DIFFRACTIONf_dihedral_angle_d12.451893
X-RAY DIFFRACTIONf_chiral_restr0.062757
X-RAY DIFFRACTIONf_plane_restr0.008936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.2581360.20863733X-RAY DIFFRACTION95
1.8-1.850.26521430.18093921X-RAY DIFFRACTION98
1.85-1.910.22841400.1743877X-RAY DIFFRACTION98
1.91-1.970.22421420.16433911X-RAY DIFFRACTION99
1.97-2.040.22151430.1543934X-RAY DIFFRACTION99
2.04-2.120.21181430.15933928X-RAY DIFFRACTION99
2.12-2.220.22391430.16063932X-RAY DIFFRACTION99
2.22-2.330.22861420.16153902X-RAY DIFFRACTION99
2.33-2.480.21681440.15933964X-RAY DIFFRACTION99
2.48-2.670.19541440.16363978X-RAY DIFFRACTION99
2.67-2.940.21871430.16033925X-RAY DIFFRACTION100
2.94-3.370.17821450.14753991X-RAY DIFFRACTION100
3.37-4.240.16891450.12434000X-RAY DIFFRACTION100
4.24-45.450.16151470.12664047X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.7554 Å / Origin y: -4.4478 Å / Origin z: 14.3024 Å
111213212223313233
T0.1204 Å20.0256 Å20.0081 Å2-0.131 Å2-0.0047 Å2--0.1146 Å2
L0.4107 °20.1263 °20.1366 °2-1.0394 °2-0.1096 °2--0.8134 °2
S-0.0286 Å °-0.0378 Å °0.0197 Å °0.042 Å °0.0329 Å °0.0194 Å °-0.0501 Å °-0.0377 Å °-0.0044 Å °
Refinement TLS groupSelection details: all

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