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- PDB-8bmy: Bacteroides thetaiotaomicron surface lipoprotein bound to cyanoco... -

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Basic information

Entry
Database: PDB / ID: 8bmy
TitleBacteroides thetaiotaomicron surface lipoprotein bound to cyanocobalamin
ComponentsPutative surface layer protein
KeywordsMEMBRANE PROTEIN / beta propeller surface protein 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
CYANOCOBALAMIN / Surface layer protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative surface layer protein
B: Putative surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,07110
Polymers79,9032
Non-polymers3,1688
Water14,862825
1
A: Putative surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5365
Polymers39,9521
Non-polymers1,5844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-50 kcal/mol
Surface area14040 Å2
MethodPISA
2
B: Putative surface layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5365
Polymers39,9521
Non-polymers1,5844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-49 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.315, 59.078, 101.544
Angle α, β, γ (deg.)90.000, 103.865, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 40 - 373 / Label seq-ID: 9 - 342

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Putative surface layer protein


Mass: 39951.637 Da / Num. of mol.: 2
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-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulphate, 0.1M Tris pH 8.5, 1.26 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 1.72→59.08 Å / Num. obs: 97918 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.099 / Rrim(I) all: 0.147 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.42-59.083.30.062979180.9920.0540.083
1.72-1.753.60.73647530.5570.6720.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSM

3dsm


Resolution: 1.72→55.072 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.178 / SU B: 5.915 / SU ML: 0.083 / Average fsc free: 0.9091 / Average fsc work: 0.9235 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2227 4849 4.955 %
Rwork0.1787 93007 -
all0.181 --
obs-97856 99.455 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.363 Å20 Å20.455 Å2
2--0.09 Å20 Å2
3----0.604 Å2
Refinement stepCycle: LAST / Resolution: 1.72→55.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 208 825 6513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135871
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155230
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.7038057
X-RAY DIFFRACTIONr_angle_other_deg1.2741.62112019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8155670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54323.168322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47215901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1911526
X-RAY DIFFRACTIONr_chiral_restr0.0650.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021460
X-RAY DIFFRACTIONr_nbd_refined0.1770.2948
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.25327
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2645
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2580.212
X-RAY DIFFRACTIONr_nbd_other0.2120.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.222
X-RAY DIFFRACTIONr_mcbond_it1.8961.8542674
X-RAY DIFFRACTIONr_mcbond_other1.8911.8532673
X-RAY DIFFRACTIONr_mcangle_it2.3842.7853340
X-RAY DIFFRACTIONr_mcangle_other2.3842.7863341
X-RAY DIFFRACTIONr_scbond_it2.4292.1083197
X-RAY DIFFRACTIONr_scbond_other2.4172.1023181
X-RAY DIFFRACTIONr_scangle_it2.9613.0564715
X-RAY DIFFRACTIONr_scangle_other2.9363.0464692
X-RAY DIFFRACTIONr_lrange_it4.09422.7036836
X-RAY DIFFRACTIONr_lrange_other3.62221.8176586
X-RAY DIFFRACTIONr_rigid_bond_restr1.356311101
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.0511760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.06740.0501
12BX-RAY DIFFRACTIONLocal ncs0.06740.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.72-1.7650.3233670.25967660.26271880.790.81899.23480.246
1.765-1.8130.2983360.24566740.24770600.8310.84599.29180.231
1.813-1.8650.2773120.2164600.21368480.8650.88898.89020.192
1.865-1.9230.2453230.18463270.18766840.8990.91699.49130.166
1.923-1.9860.2393020.17660620.17964270.9070.92399.01980.156
1.986-2.0550.2292770.16759430.1762680.9190.93599.23420.151
2.055-2.1330.2143010.15956880.16160200.9270.94599.48510.143
2.133-2.220.2282790.15955350.16258340.9220.9499.65720.146
2.22-2.3180.2212910.15252260.15655650.9260.94799.13750.142
2.318-2.4310.2072740.14250490.14553420.940.95699.64430.133
2.431-2.5620.2122420.14448000.14750660.9390.95499.52630.136
2.562-2.7180.1962460.15545460.15747970.9430.95299.89580.15
2.718-2.9050.2242480.17142840.17445370.9370.9599.88980.169
2.905-3.1370.2142010.18939930.1942020.9360.94199.80960.19
3.137-3.4350.2132150.1936750.19139050.9440.94899.61590.199
3.435-3.8390.1851690.17233590.17335290.950.95699.97170.186
3.839-4.4290.191660.16129690.16331360.9590.96399.96810.186
4.429-5.4150.1861230.16725300.16826530.9680.9721000.194
5.415-7.6220.2871090.24919640.25120790.9350.93999.71140.277
7.622-55.0720.299680.2911430.2912140.9290.93499.75290.349

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