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- PDB-8y5v: GII.4 Sydney PD and 2'-FL -

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Basic information

Entry
Database: PDB / ID: 8y5v
TitleGII.4 Sydney PD and 2'-FL
ComponentsGII.4 Sydney PD in complex with 2'-FL (powder)
KeywordsVIRAL PROTEIN / Sugar / complex / milk oligosaccharide
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsHansman, G. / Tame, J.R.H. / Kher, G. / Pancera, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Virol. / Year: 2024
Title: Human milk oligosaccharide 2'-fucosyllactose guards norovirus histo-blood group antigen co-factor binding site.
Authors: Rudd, P.A. / Kher, G. / Tame, J.R.H. / Irie, H. / Haselhorst, T. / von Itzstein, M. / Pancera, M. / Hansman, G.S.
History
DepositionFeb 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GII.4 Sydney PD in complex with 2'-FL (powder)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0187
Polymers34,2191
Non-polymers7996
Water6,125340
1
A: GII.4 Sydney PD in complex with 2'-FL (powder)
hetero molecules

A: GII.4 Sydney PD in complex with 2'-FL (powder)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,03614
Polymers68,4382
Non-polymers1,59812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area3300 Å2
ΔGint-11 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.624, 55.763, 63.613
Angle α, β, γ (deg.)90.00, 120.14, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein GII.4 Sydney PD in complex with 2'-FL (powder)


Mass: 34219.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE GENEBANK ACCESSION NUMBER IS JX459908 for this protein.
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli)
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: magnesium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.54→47.02 Å / Num. obs: 42181 / % possible obs: 95.3 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.034 / Rrim(I) all: 0.076 / Χ2: 0.53 / Net I/σ(I): 11 / Num. measured all: 200633
Reflection shellResolution: 1.54→1.56 Å / % possible obs: 86.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.96 / Num. measured all: 8710 / Num. unique obs: 1890 / CC1/2: 0.601 / Rpim(I) all: 0.489 / Rrim(I) all: 1.08 / Χ2: 0.47 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→41.69 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 2107 5 %
Rwork0.1547 --
obs0.1561 42174 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 53 340 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092491
X-RAY DIFFRACTIONf_angle_d1.0653402
X-RAY DIFFRACTIONf_dihedral_angle_d13.36896
X-RAY DIFFRACTIONf_chiral_restr0.227386
X-RAY DIFFRACTIONf_plane_restr0.011444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.29761160.26972459X-RAY DIFFRACTION88
1.57-1.610.26331470.23742678X-RAY DIFFRACTION95
1.61-1.660.26771480.21782656X-RAY DIFFRACTION95
1.66-1.710.24271290.19922676X-RAY DIFFRACTION95
1.71-1.760.2271400.18162703X-RAY DIFFRACTION96
1.76-1.820.21791450.16892663X-RAY DIFFRACTION96
1.82-1.90.19371410.16172654X-RAY DIFFRACTION95
1.9-1.980.18991360.16062623X-RAY DIFFRACTION93
1.98-2.090.15711380.15282539X-RAY DIFFRACTION91
2.09-2.220.17211420.14432751X-RAY DIFFRACTION97
2.22-2.390.19951490.14082729X-RAY DIFFRACTION97
2.39-2.630.18121420.14852745X-RAY DIFFRACTION97
2.63-3.010.19121470.1472735X-RAY DIFFRACTION97
3.01-3.790.15911370.14132629X-RAY DIFFRACTION92
3.79-41.690.15421500.13842827X-RAY DIFFRACTION98

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