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- PDB-9uu0: The structure of Bacteroides fragilis T6SS effector BteO -

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Basic information

Entry
Database: PDB / ID: 9uu0
TitleThe structure of Bacteroides fragilis T6SS effector BteO
ComponentsMaltose/maltodextrin-binding periplasmic protein,Bacteroides fragilis T6SS effector
KeywordsTOXIN / Bacteroides fragilis T6SS effector
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsHe, J. / Gao, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: A nonenzymatic effector disrupts Bacteroides cell wall homeostasis via OmpA targeting to mediate interbacterial competition.
Authors: He, J. / Chen, Z. / Jiang, K. / Yang, Y. / Li, W. / Wang, X. / Xu, X. / Zheng, S. / Jiao, X. / Chen, X. / Huo, L. / Lim, B. / Liu, S.J. / Gao, X.
History
DepositionMay 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Bacteroides fragilis T6SS effector
B: Maltose/maltodextrin-binding periplasmic protein,Bacteroides fragilis T6SS effector


Theoretical massNumber of molelcules
Total (without water)130,6052
Polymers130,6052
Non-polymers00
Water39622
1
A: Maltose/maltodextrin-binding periplasmic protein,Bacteroides fragilis T6SS effector


Theoretical massNumber of molelcules
Total (without water)65,3021
Polymers65,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose/maltodextrin-binding periplasmic protein,Bacteroides fragilis T6SS effector


Theoretical massNumber of molelcules
Total (without water)65,3021
Polymers65,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)234.120, 63.460, 113.610
Angle α, β, γ (deg.)90.000, 110.786, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Bacteroides fragilis T6SS effector / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 65302.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: During the experiment, author express the MBP-BteO protein using the truncation 27-392 of MBP and the truncation 83-294 of BteO fused to a C-terminal His-tag expression vector with 11 animo ...Details: During the experiment, author express the MBP-BteO protein using the truncation 27-392 of MBP and the truncation 83-294 of BteO fused to a C-terminal His-tag expression vector with 11 animo acids linker between MBP and BteO. Chain A/B residues 379 to 590: NCBI Reference Sequence: WP_025814153.1 residues 83 to 294
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Bacteroides fragilis (bacteria)
Gene: malE, b4034, JW3994 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1M sodium citrate pH 3.9, 12% w/v PEG35000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.72→56.26 Å / Num. obs: 42024 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 61.45 Å2 / Rpim(I) all: 0.093 / Rrim(I) all: 0.246 / Net I/σ(I): 7.7
Reflection shellResolution: 2.72→2.817 Å / Num. unique obs: 42024 / Rrim(I) all: 0.246

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXphasing
PHENIX1.17.1_3660refinement
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→56.26 Å / SU ML: 0.5044 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.2876
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2966 2087 4.97 %
Rwork0.2748 39905 -
obs0.2759 41992 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.74 Å2
Refinement stepCycle: LAST / Resolution: 2.72→56.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9212 0 0 22 9234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319416
X-RAY DIFFRACTIONf_angle_d0.589112756
X-RAY DIFFRACTIONf_chiral_restr0.04551376
X-RAY DIFFRACTIONf_plane_restr0.00271666
X-RAY DIFFRACTIONf_dihedral_angle_d12.53233446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.780.45731300.43832638X-RAY DIFFRACTION98.93
2.78-2.850.45531540.43422607X-RAY DIFFRACTION98.93
2.85-2.930.43191360.42162616X-RAY DIFFRACTION98.92
2.93-3.020.44791550.39342670X-RAY DIFFRACTION98.88
3.02-3.110.37691180.3922639X-RAY DIFFRACTION99.21
3.11-3.220.37171390.36192638X-RAY DIFFRACTION99
3.22-3.350.36151380.34092671X-RAY DIFFRACTION99.22
3.35-3.510.37771360.31712641X-RAY DIFFRACTION99.32
3.51-3.690.30251500.29152659X-RAY DIFFRACTION99.29
3.69-3.920.30211350.27282658X-RAY DIFFRACTION99.4
3.92-4.230.30611340.25562667X-RAY DIFFRACTION99.29
4.23-4.650.2691280.22772677X-RAY DIFFRACTION99.4
4.65-5.320.24811610.22462676X-RAY DIFFRACTION99.3
5.32-6.70.23971390.24652687X-RAY DIFFRACTION99.02
6.71-100.18951340.19332761X-RAY DIFFRACTION97.8

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