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- PDB-8bn0: Bacteroides thetaiotaomicron surface protein BT1954 bound to -

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Basic information

Entry
Database: PDB / ID: 8bn0
TitleBacteroides thetaiotaomicron surface protein BT1954 bound to
ComponentsPutative surface layer protein
KeywordsMEMBRANE PROTEIN / Surface exposed protein Beta propeller Vitamin B12 binding protein
Function / homology
Function and homology information


Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / : / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
COB(II)INAMIDE / CYANIDE ION / Surface layer protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsAbellon-Ruiz, J. / Jana, K. / Silale, A. / Basle, A. / Kleinekathofer, U. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT 214222/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B uptake in gut Bacteroides.
Authors: Javier Abellon-Ruiz / Kalyanashis Jana / Augustinas Silale / Andrew M Frey / Arnaud Baslé / Matthias Trost / Ulrich Kleinekathöfer / Bert van den Berg /
Abstract: Vitamin B (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition ...Vitamin B (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B outer membrane transporters together with a conserved array of surface-exposed B-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B with high affinities. Closing of the BtuG lid following B capture causes destabilisation of the bound B by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.
History
DepositionNov 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6844
Polymers43,6321
Non-polymers1,0523
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-13 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.050, 79.050, 155.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Putative surface layer protein


Mass: 43632.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Gene: BT_1954 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6D0
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H72CoN11O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1M Na malonate pH7.0 0.1M HEPES pH 7.0 0.5% Jefamine ED2001 pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.33→43.3 Å / Num. obs: 113086 / % possible obs: 99.85 % / Redundancy: 24.2 % / Biso Wilson estimate: 18.53 Å2 / CC1/2: 1 / Net I/σ(I): 16.7
Reflection shellResolution: 1.33→1.36 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 11000 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
PHENIX1.20rc3_4406refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSM

3dsm


Resolution: 1.33→43.3 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1672 5698 5.04 %
Rwork0.1411 107371 -
obs0.1424 113069 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 1.33→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 71 414 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212977
X-RAY DIFFRACTIONf_angle_d1.35134074
X-RAY DIFFRACTIONf_chiral_restr0.1276418
X-RAY DIFFRACTIONf_plane_restr0.0095518
X-RAY DIFFRACTIONf_dihedral_angle_d9.395410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.31951910.3143409X-RAY DIFFRACTION96.77
1.35-1.360.33341830.30653516X-RAY DIFFRACTION99.14
1.36-1.380.34791730.30213517X-RAY DIFFRACTION99.97
1.38-1.390.31131930.28313534X-RAY DIFFRACTION100
1.39-1.410.30831750.26163551X-RAY DIFFRACTION100
1.41-1.430.2511960.23673531X-RAY DIFFRACTION100
1.43-1.450.27861880.23153532X-RAY DIFFRACTION100
1.45-1.470.23252080.2083526X-RAY DIFFRACTION100
1.47-1.50.20761900.17913540X-RAY DIFFRACTION100
1.5-1.520.22682050.17593521X-RAY DIFFRACTION100
1.52-1.550.20352220.16183516X-RAY DIFFRACTION100
1.55-1.580.17031920.14023541X-RAY DIFFRACTION100
1.58-1.610.16541570.13673601X-RAY DIFFRACTION99.97
1.61-1.640.16071700.12793557X-RAY DIFFRACTION100
1.64-1.680.15571930.12473540X-RAY DIFFRACTION100
1.68-1.710.16421680.12133589X-RAY DIFFRACTION100
1.71-1.760.1651630.12273606X-RAY DIFFRACTION100
1.76-1.810.17342020.12993566X-RAY DIFFRACTION100
1.81-1.860.15472140.12343515X-RAY DIFFRACTION100
1.86-1.920.15231890.12473589X-RAY DIFFRACTION100
1.92-1.990.14781880.11463582X-RAY DIFFRACTION99.89
1.99-2.070.15121830.11913586X-RAY DIFFRACTION99.97
2.07-2.160.15121810.11943602X-RAY DIFFRACTION100
2.16-2.270.14541620.1283630X-RAY DIFFRACTION99.92
2.27-2.420.15672020.13013605X-RAY DIFFRACTION99.97
2.42-2.60.16481940.13863636X-RAY DIFFRACTION100
2.6-2.870.16372040.14813626X-RAY DIFFRACTION100
2.87-3.280.17831980.15083670X-RAY DIFFRACTION100
3.28-4.130.14492030.12553714X-RAY DIFFRACTION99.97
4.13-43.30.15412110.13363923X-RAY DIFFRACTION99.95

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