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- PDB-9jdi: Crystal structure of the type VI secretion system effector-immuni... -

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Basic information

Entry
Database: PDB / ID: 9jdi
TitleCrystal structure of the type VI secretion system effector-immunity complex BtpeA CTD-BtpiA from Bacteroides fragilis.
Components
  • BtpiA
  • DUF3289 family protein
KeywordsANTIMICROBIAL PROTEIN / Bacteroides fragilis / T6SS / Effector / Immunity / Phosphatase
Function / homologyConserved hypothetical protein CHP03034 / Protein of unknown function DUF4280 / Protein of unknown function (DUF3289) / Domain of unknown function (DUF4280) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein / DUF3289 family protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsZheng, S.N. / Li, W.X. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)323B2003 China
CitationJournal: To Be Published
Title: Synergistic Function and Effector-Dependent Secretion in the Type VI Secretion System
Authors: Li, W.X. / Zheng, S.N. / Chen, Z. / Gao, X.
History
DepositionAug 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF3289 family protein
C: BtpiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3014
Polymers63,1162
Non-polymers1842
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-7 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.926, 67.114, 87.374
Angle α, β, γ (deg.)90.000, 95.450, 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 DUF3289 family protein / BtpeA CTD


Mass: 41700.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12460 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6JKA9
#2: Protein BtpiA


Mass: 21415.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Immunity of BtpeA, the T6SS effector protein of Bacteroides fragilis.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HE89
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Citrate (PH=5.0), 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.11→56.71 Å / Num. obs: 36002 / % possible obs: 94.64 % / Redundancy: 6.1 % / Biso Wilson estimate: 30.94 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.3
Reflection shellResolution: 2.11→2.18 Å / Num. unique obs: 3772 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot1.20.1_4487model building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→56.71 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1756 4.88 %
Rwork0.1856 34246 -
obs0.1873 36002 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.56 Å2
Refinement stepCycle: LAST / Resolution: 2.11→56.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 12 375 4493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274205
X-RAY DIFFRACTIONf_angle_d0.48955664
X-RAY DIFFRACTIONf_chiral_restr0.0423603
X-RAY DIFFRACTIONf_plane_restr0.0027722
X-RAY DIFFRACTIONf_dihedral_angle_d15.09071574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.29511350.24242723X-RAY DIFFRACTION99.9
2.17-2.230.29971260.22432809X-RAY DIFFRACTION99.63
2.23-2.30.2889500.2181365X-RAY DIFFRACTION49.08
2.3-2.380.26611410.22442764X-RAY DIFFRACTION99.93
2.38-2.480.27261330.21742776X-RAY DIFFRACTION99.97
2.48-2.590.31331330.22042785X-RAY DIFFRACTION100
2.59-2.730.26761240.21882298X-RAY DIFFRACTION83.06
2.73-2.90.25931340.19742804X-RAY DIFFRACTION99.93
2.9-3.120.20091370.19372764X-RAY DIFFRACTION100
3.12-3.440.20221540.17772780X-RAY DIFFRACTION99.9
3.44-3.930.20561500.15642798X-RAY DIFFRACTION99.86
3.93-4.960.18221780.14972754X-RAY DIFFRACTION99.86
4.96-56.710.18711610.18692826X-RAY DIFFRACTION98.74

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