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- PDB-9jdh: Crystal structure of the T6SS effector BtaeB-NTD from Bacteroides... -

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Basic information

Entry
Database: PDB / ID: 9jdh
TitleCrystal structure of the T6SS effector BtaeB-NTD from Bacteroides fragilis
ComponentsPeptidase C39-like domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / Bacteroides fragilis / T6SS / effector / Interbacterial antagonism
Function / homologyDI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3915
Polymers43,9661
Non-polymers4244
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.670, 49.370, 183.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 43966.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BtaeB N-terminal domain of the T6ss effector of Bacteroides fragilis.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: FSA06_12440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6HES3
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium acetate (PH=5.2), 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.18→91.88 Å / Num. obs: 21523 / % possible obs: 99.73 % / Redundancy: 12.2 % / Biso Wilson estimate: 38.45 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.7
Reflection shellResolution: 2.18→2.26 Å / Num. unique obs: 2083 / CC1/2: 0.658

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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: 2.18→91.88 Å / SU ML: 0.2885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 1066 4.95 %
Rwork0.1999 20453 -
obs0.2023 21519 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.4 Å2
Refinement stepCycle: LAST / Resolution: 2.18→91.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 28 141 3185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273097
X-RAY DIFFRACTIONf_angle_d0.57544162
X-RAY DIFFRACTIONf_chiral_restr0.0489464
X-RAY DIFFRACTIONf_plane_restr0.0042530
X-RAY DIFFRACTIONf_dihedral_angle_d16.91461174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.280.31871260.24362499X-RAY DIFFRACTION99.62
2.28-2.40.28881300.21572494X-RAY DIFFRACTION99.89
2.4-2.550.26111270.22352533X-RAY DIFFRACTION99.89
2.55-2.750.28641260.22422560X-RAY DIFFRACTION99.85
2.75-3.020.24461370.21012503X-RAY DIFFRACTION99.96
3.02-3.460.26121500.20272550X-RAY DIFFRACTION99.93
3.46-4.360.23451530.17822581X-RAY DIFFRACTION99.78
4.36-91.880.21841170.19222733X-RAY DIFFRACTION99.03

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