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- PDB-9uu1: Bacteroides fragilis T6SS immunity protein BtiO -

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Basic information

Entry
Database: PDB / ID: 9uu1
TitleBacteroides fragilis T6SS immunity protein BtiO
ComponentsBacteroides fragilis T6SS immunity protein BtiO
KeywordsANTITOXIN / Bacteroides fragilis T6SS immunity protein
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. / Gao, X.
History
DepositionMay 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteroides fragilis T6SS immunity protein BtiO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7702
Polymers12,7101
Non-polymers601
Water77543
1
A: Bacteroides fragilis T6SS immunity protein BtiO
hetero molecules

A: Bacteroides fragilis T6SS immunity protein BtiO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5414
Polymers25,4212
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.251, 41.251, 124.961
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Bacteroides fragilis T6SS immunity protein BtiO


Mass: 12710.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: During the experiment, author express the BtiO protein using the truncation 23-135 fused to a C-terminal His-tag expression vector. However, as noted, there are 3 segments of the sequence ...Details: During the experiment, author express the BtiO protein using the truncation 23-135 fused to a C-terminal His-tag expression vector. However, as noted, there are 3 segments of the sequence that is not visible in the density map. This unobserved region is due to disorder and thus could not be modeled in the final structure. The missing segment corresponds to residues C23-N25, N80-D86 and K134-Q135 of Bte1 which were not visible in the electron density map. This was noted during the refinement process, and no electron density was observed for this region, making it impossible to include in the final model. Chain A residues 5-58: NCBI Reference Sequence: WP_025814152.1 residues 24 to 79 Chain A residues 66-113: NCBI Reference Sequence: WP_025814152.1 residues 87 to 133
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 20% v/v 2-propanol, 0.1M MES monohydrate pH 6.0, 20% w/v PEG MME 2000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→23.52 Å / Num. obs: 8809 / % possible obs: 96.7 % / Redundancy: 14.3 % / Biso Wilson estimate: 39.65 Å2 / CC1/2: 0.993 / Net I/σ(I): 1.5
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 8809 / Rrim(I) all: 0.683

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.17.1_3660refinement
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.52 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 850 9.88 %
Rwork0.2037 7752 -
obs0.2074 8602 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.41 Å2
Refinement stepCycle: LAST / Resolution: 2→23.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 4 43 875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077851
X-RAY DIFFRACTIONf_angle_d0.78741146
X-RAY DIFFRACTIONf_chiral_restr0.0567119
X-RAY DIFFRACTIONf_plane_restr0.0046142
X-RAY DIFFRACTIONf_dihedral_angle_d6.1715109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.120.27881330.23081202X-RAY DIFFRACTION92.97
2.12-2.290.2621350.21911246X-RAY DIFFRACTION94.91
2.29-2.520.23091320.21541258X-RAY DIFFRACTION96.53
2.52-2.880.26071410.22261304X-RAY DIFFRACTION98.17
2.88-3.630.22651440.21061341X-RAY DIFFRACTION99.2
3.63-23.520.241650.18931401X-RAY DIFFRACTION98.24
Refinement TLS params.Method: refined / Origin x: 28.0669539244 Å / Origin y: -13.8435728435 Å / Origin z: 9.69312935728 Å
111213212223313233
T0.377626571933 Å2-0.0252370602276 Å2-0.0162528353755 Å2-0.368146671583 Å20.038961988423 Å2--0.353311800473 Å2
L0.803953530244 °2-0.318963292744 °20.563171741404 °2-1.06693714539 °2-0.375278580267 °2--1.05555629884 °2
S0.140674417947 Å °-0.0125230428049 Å °0.0455380976297 Å °-0.0120956093473 Å °-0.0487834734013 Å °0.0360391276229 Å °-0.0215545033547 Å °-0.0138627624801 Å °0.000254787482425 Å °
Refinement TLS groupSelection details: all

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