9JDD | pdb_00009jdd

Crystal structure of the type VI secretion system effector-immunity complex BtaeB CTD-BtaiB from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb9JDD/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-31 Released: 2025-09-03 
• Deposition Author(s): Zheng, S.N., Li, W.X., Chen, Z., Gao, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: in silico

Literature

Synergistic Function and Effector-Dependent Secretion in the Type VI Secretion System

Li, W.X., Zheng, S.N., Gao, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.3 kDa 
• Atom Count: 2,954 
• Modeled Residue Count: 315 
• Deposited Residue Count: 354 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C39-like domain-containing protein	A	211	Bacteroides fragilis	Mutation(s): 0  Gene Names: FSA06_12440
UniProt
Find proteins for A0AB38PQQ6 (Bacteroides fragilis) Explore A0AB38PQQ6  Go to UniProtKB:  A0AB38PQQ6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BtaiB	B	143	Bacteroides fragilis	Mutation(s): 0  Gene Names: FSA06_12435
UniProt
Find proteins for A0A5C6HFH9 (Bacteroides fragilis) Explore A0A5C6HFH9  Go to UniProtKB:  A0A5C6HFH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.385	α = 90
b = 117.385	β = 90
c = 141.493	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Zheng, S.N., Li, W.X., Chen, Z., Gao, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	323B2003

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release