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- PDB-7nox: Structure of SGBP BO2743 from Bacteroides ovatus in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7nox
TitleStructure of SGBP BO2743 from Bacteroides ovatus in complex with mixed-linked gluco-nonasaccharide
ComponentsSurface glycan-binding protein BO2743
KeywordsSUGAR BINDING PROTEIN / Bacteroides ovatus / surface glycan binding protein (SGBP) / SusD-homologue / Polysaccharide Utilization Loci (PUL) / gut microbiota / beta-glucans / barley-9
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / AZIDE ION / TRIETHYLENE GLYCOL / SusD/RagB family nutrient-binding outer membrane lipoprotein
Function and homology information
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsCorreia, V.C. / Trovao, F. / Pinheiro, B.A. / Palma, A.S. / Carvalho, A.L.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)PTDC/BIA-MIB/31730/2017 Portugal
Foundation for Science and Technology (FCT)RECI/BBB-BEP/0124/2012 Portugal
CitationJournal: Microbiol Spectr / Year: 2021
Title: Mapping Molecular Recognition of beta 1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus.
Authors: Correia, V.G. / Trovao, F. / Pinheiro, B.A. / Bras, J.L.A. / Silva, L.M. / Nunes, C. / Coimbra, M.A. / Liu, Y. / Feizi, T. / Fontes, C.M.G.A. / Mulloy, B. / Chai, W. / Carvalho, A.L. / Palma, A.S.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface glycan-binding protein BO2743
B: Surface glycan-binding protein BO2743
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,32237
Polymers135,8372
Non-polymers5,48535
Water17,835990
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint62 kcal/mol
Surface area37280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.842, 88.437, 156.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Surface glycan-binding protein BO2743


Mass: 67918.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_02743 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7LY27
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,9,8/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1/a3-b1_b4-c1_c4-d1_d3-e1_e4-f1_f4-g1_g3-h1_h4-i1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 1023 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: N3
#8: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 8 mg/mL; 25% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 mM MgCl2.6H2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.43→62.32 Å / Num. obs: 175289 / % possible obs: 96.5 % / Redundancy: 9 % / CC1/2: 1 / Net I/σ(I): 1.6
Reflection shellResolution: 1.43→1.55 Å / Num. unique obs: 8764 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
STARANISOdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J5U

5j5u


Resolution: 1.43→44.86 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1897 8680 -
Rwork0.1616 --
obs-175274 78.35 %
Displacement parametersBiso max: 80.83 Å2 / Biso mean: 23.0947 Å2 / Biso min: 10.51 Å2
Refinement stepCycle: LAST / Resolution: 1.43→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 368 992 9585
LS refinement shellResolution: 1.43→1.45 Å
RfactorNum. reflection% reflection
Rfree0.4049 --
Rwork0.3391 --
obs-302 4 %

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