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

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Basic information

Entry
Database: PDB / ID: 9jdd
TitleCrystal structure of the type VI secretion system effector-immunity complex BtaeB CTD-BtaiB from Bacteroides fragilis
Components
  • BtaiB
  • Peptidase C39-like domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / T6SS / effector / immunity / Bacteroides fragilis / C39-like peptidase
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / : / Lipoprotein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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. / 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: Peptidase C39-like domain-containing protein
B: BtaiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3054
Polymers41,1732
Non-polymers1322
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-4 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.385, 117.385, 141.493
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Peptidase C39-like domain-containing protein / BtaeB_CTD


Mass: 23739.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BtaeB can be divided into a function unknown N-terminal domain (NTD) and a C-terminal domain (CTD) belonging to the characterized C39 family peptidase.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HES3
#2: Protein BtaiB


Mass: 17433.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12435 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HFH9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.05 M BIS-TRIS (PH=5,9), 0.05 M (NH4)2SO4, 28% Pentaerythritol ethoxylate (15/4 EO/OH)

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→30.56 Å / Num. obs: 44681 / % possible obs: 97.53 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 1 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.96 Å / Num. unique obs: 4267 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.56 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1906 2000 4.48 %
Rwork0.1597 42681 -
obs0.1611 44681 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 7 373 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01862644
X-RAY DIFFRACTIONf_angle_d1.43173581
X-RAY DIFFRACTIONf_chiral_restr0.1035378
X-RAY DIFFRACTIONf_plane_restr0.0115459
X-RAY DIFFRACTIONf_dihedral_angle_d15.2652967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.24671370.21922912X-RAY DIFFRACTION94.93
1.95-20.23791370.20172943X-RAY DIFFRACTION96.01
2-2.060.26281400.19882980X-RAY DIFFRACTION96.86
2.06-2.130.22421390.18872955X-RAY DIFFRACTION96.84
2.13-2.20.22191390.17242982X-RAY DIFFRACTION96.87
2.2-2.290.20671400.16192999X-RAY DIFFRACTION97.12
2.29-2.390.20631410.16223010X-RAY DIFFRACTION97.37
2.39-2.520.20621420.15633017X-RAY DIFFRACTION97.74
2.52-2.680.1831430.16063059X-RAY DIFFRACTION98.04
2.68-2.890.16381430.15633055X-RAY DIFFRACTION98.22
2.89-3.180.17981460.15533103X-RAY DIFFRACTION98.69
3.18-3.630.18861460.153119X-RAY DIFFRACTION98.76
3.63-4.580.1631490.12973179X-RAY DIFFRACTION99.11
4.58-30.560.1811580.16673368X-RAY DIFFRACTION99.3

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