9XVW | pdb_00009xvw

Crystal structure of mature Bacteroides fragilis toxin 2

• PDB DOI: https://doi.org/10.2210/pdb9XVW/pdb

• Classification: TOXIN
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-11-27 Released: 2026-01-07 
• Deposition Author(s): Fu, G., Zhao, X., Chai, Y., Wang, L.
• Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.272 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of mature Bacteroides fragilis toxin 2

Fu, G., Zhao, X., Chai, Y., Wang, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.74 kDa 
• Atom Count: 3,155 
• Modeled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bft	A [auth B], B [auth A]	194	Bacteroides fragilis	Mutation(s): 0  Gene Names: bft
UniProt
Find proteins for Q6UCA5 (Bacteroides fragilis) Explore Q6UCA5  Go to UniProtKB:  Q6UCA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.272 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.122	α = 90
b = 47.122	β = 90
c = 148.045	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-07 
Deposition Author(s): Fu, G., Zhao, X., Chai, Y., Wang, L.

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Funding Organization	Location	Grant Number
Other government	China	2020YFA0509202, 2025YFC2311800
National Natural Science Foundation of China (NSFC)	China	82222040
Chinese Academy of Sciences	China	YSBR-083

Revision History  

• Version 1.0: 2026-01-07
  Type: Initial release