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

Experimental Data Snapshot

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

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of mature Bacteroides fragilis toxin 2

Fu, G., Zhao, X., Chai, Y., Wang, L.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6UCA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272 (Depositor), 0.272 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-07

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.