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- PDB-7o8c: Structure of SGBP BO2743 from Bacteroides ovatus -

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Basic information

Entry
Database: PDB / ID: 7o8c
TitleStructure of SGBP BO2743 from Bacteroides ovatus
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 / homology
Function and homology information


SusD-like 2 / Starch-binding associating with outer membrane / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
AZIDE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / SusD/RagB family nutrient-binding outer membrane lipoprotein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionApr 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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)138,85634
Polymers135,8372
Non-polymers3,01932
Water9,800544
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-134 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.120, 207.120, 170.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 2 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 (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153) (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02743 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7LY27

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Non-polymers , 6 types, 576 molecules

#2: Chemical
ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 13.7 mg/mL; 2.0 M Ammonium Sulphate, 0.1 M BIS-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2→55.56 Å / Num. obs: 123741 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 0.845 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 9068 / CC1/2: 0.338

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Processing

Software
NameVersionClassification
PDB-REDO1.19.1_4122refinement
PHENIX1.19.1_4122refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J5U

5j5u


Resolution: 2→55.56 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 23.0006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 6114 4.94 %
Rwork0.2006 117583 -
obs0.202 123697 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.57 Å2
Refinement stepCycle: LAST / Resolution: 2→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9268 0 170 544 9982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00769650
X-RAY DIFFRACTIONf_angle_d0.879913063
X-RAY DIFFRACTIONf_chiral_restr0.04851371
X-RAY DIFFRACTIONf_plane_restr0.00721704
X-RAY DIFFRACTIONf_dihedral_angle_d8.07231332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.33162200.31383851X-RAY DIFFRACTION100
2.02-2.050.33922230.31753895X-RAY DIFFRACTION100
2.05-2.070.34051820.3173869X-RAY DIFFRACTION99.9
2.07-2.10.32952230.29993880X-RAY DIFFRACTION100
2.1-2.130.30661940.29183879X-RAY DIFFRACTION100
2.13-2.150.29711980.27923911X-RAY DIFFRACTION100
2.15-2.190.29612080.2683866X-RAY DIFFRACTION100
2.19-2.220.26661950.25463893X-RAY DIFFRACTION99.98
2.22-2.250.30381980.25483897X-RAY DIFFRACTION100
2.25-2.290.26831910.23223888X-RAY DIFFRACTION100
2.29-2.330.22561990.21983907X-RAY DIFFRACTION100
2.33-2.370.23352150.21393872X-RAY DIFFRACTION100
2.37-2.420.24441980.21283935X-RAY DIFFRACTION99.93
2.42-2.470.28061790.21113893X-RAY DIFFRACTION99.98
2.47-2.520.24181760.20883932X-RAY DIFFRACTION99.9
2.52-2.580.22892260.20153857X-RAY DIFFRACTION100
2.58-2.640.23852170.19623895X-RAY DIFFRACTION99.98
2.64-2.710.25671820.19353926X-RAY DIFFRACTION99.95
2.71-2.790.24951970.21043928X-RAY DIFFRACTION99.95
2.79-2.880.27582080.21413905X-RAY DIFFRACTION99.95
2.88-2.990.23772350.2023894X-RAY DIFFRACTION99.98
2.99-3.110.2381840.19783929X-RAY DIFFRACTION99.98
3.11-3.250.23032040.19163932X-RAY DIFFRACTION100
3.25-3.420.21231630.19573924X-RAY DIFFRACTION98.93
3.42-3.630.21452450.18023916X-RAY DIFFRACTION99.71
3.63-3.910.19352230.16773918X-RAY DIFFRACTION100
3.91-4.310.18282230.15793952X-RAY DIFFRACTION100
4.31-4.930.17582090.16113998X-RAY DIFFRACTION100
4.93-6.210.20572030.18734029X-RAY DIFFRACTION100
6.21-55.560.2021960.17594212X-RAY DIFFRACTION99.62

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