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- PDB-8y6c: Norovirus GII.10 P domain and 2'-FL (powder) -

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Basic information

Entry
Database: PDB / ID: 8y6c
TitleNorovirus GII.10 P domain and 2'-FL (powder)
ComponentsGII.10 norovirus P domain in complex with 2'FL (powder)
KeywordsVIRAL PROTEIN / Sugar / complex / milk oligosaccharide
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 2, 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.10 norovirus P domain in complex with 2'FL (powder)
B: GII.10 norovirus P domain in complex with 2'FL (powder)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,05629
Polymers69,0132
Non-polymers3,04327
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.988, 78.700, 70.770
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein GII.10 norovirus P domain in complex with 2'FL (powder)


Mass: 34506.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE GENEBANK ACCESSION NUMBER IS AF504671 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.: 3
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.: 22
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.67 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium nitrate 0.1 M bis-tris propane (pH 7.5) 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 1.47→44.63 Å / Num. obs: 122545 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.035 / Rrim(I) all: 0.075 / Χ2: 0.51 / Net I/σ(I): 9.2 / Num. measured all: 556487
Reflection shellResolution: 1.47→1.49 Å / % possible obs: 84.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.313 / Num. measured all: 21864 / Num. unique obs: 5094 / CC1/2: 0.395 / Rpim(I) all: 0.702 / Rrim(I) all: 1.494 / Χ2: 0.41 / Net I/σ(I) obs: 0.7

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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: 1.47→44.63 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 6113 4.99 %
Rwork0.1666 --
obs0.1678 122490 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 201 688 5678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095110
X-RAY DIFFRACTIONf_angle_d1.0046959
X-RAY DIFFRACTIONf_dihedral_angle_d13.4931857
X-RAY DIFFRACTIONf_chiral_restr0.296806
X-RAY DIFFRACTIONf_plane_restr0.013894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.32491530.30722988X-RAY DIFFRACTION76
1.49-1.50.32291930.29223870X-RAY DIFFRACTION100
1.5-1.520.28642160.27253889X-RAY DIFFRACTION100
1.52-1.540.26692180.26273910X-RAY DIFFRACTION100
1.54-1.560.26981830.25753871X-RAY DIFFRACTION100
1.56-1.580.27412130.24013909X-RAY DIFFRACTION100
1.58-1.60.24512110.22743905X-RAY DIFFRACTION100
1.6-1.630.22862020.22783863X-RAY DIFFRACTION100
1.63-1.650.27392070.23133900X-RAY DIFFRACTION99
1.65-1.680.26192020.22953885X-RAY DIFFRACTION100
1.68-1.710.24261980.21093909X-RAY DIFFRACTION100
1.71-1.740.22092160.19023889X-RAY DIFFRACTION100
1.74-1.770.20971970.18093911X-RAY DIFFRACTION100
1.77-1.810.2032040.17363911X-RAY DIFFRACTION100
1.81-1.850.19552140.16353907X-RAY DIFFRACTION100
1.85-1.890.20272040.16783920X-RAY DIFFRACTION100
1.89-1.940.1831960.16283902X-RAY DIFFRACTION100
1.94-1.990.18482140.16273900X-RAY DIFFRACTION100
1.99-2.050.17972040.16133921X-RAY DIFFRACTION100
2.05-2.120.18442160.16263930X-RAY DIFFRACTION100
2.12-2.190.18741950.16293913X-RAY DIFFRACTION100
2.19-2.280.1832080.15683900X-RAY DIFFRACTION100
2.28-2.390.19962070.15233921X-RAY DIFFRACTION100
2.39-2.510.18551970.16423915X-RAY DIFFRACTION100
2.51-2.670.19592040.15933919X-RAY DIFFRACTION100
2.67-2.870.19832200.16143913X-RAY DIFFRACTION100
2.87-3.160.15172030.15633926X-RAY DIFFRACTION99
3.16-3.620.16722100.15263948X-RAY DIFFRACTION100
3.62-4.560.15592070.13113928X-RAY DIFFRACTION99
4.56-44.630.18762010.15854004X-RAY DIFFRACTION99

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