8WEO

Bacteroides fragilis toxin in complex with neutralization nanobody

• PDB DOI: https://doi.org/10.2210/pdb8WEO/pdb

• Classification: TOXIN/IMMUNE SYSTEM
• Organism(s): Bacteroides fragilis, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-18 Released: 2024-09-25 
• Deposition Author(s): Guo, Y., Wen, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.197 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Bacteroides fragilis toxin in complex with neutralization nanobody

Guo, Y., Wen, Y.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 69.56 kDa 
• Atom Count: 5,713 
• Modelled Residue Count: 618 
• Deposited Residue Count: 624 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fragilysin	A [auth B], C [auth A]	186	Bacteroides fragilis	Mutation(s): 0  Gene Names: btfP EC: 3.4.24.74
UniProt
Find proteins for P54355 (Bacteroides fragilis) Explore P54355  Go to UniProtKB:  P54355

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NB243	B [auth C], D	126	Vicugna pacos	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.197 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.678	α = 90
b = 121.678	β = 90
c = 84.143	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Guo, Y., Wen, Y.

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

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release