9BIW | pdb_00009biw

Crystal structure of Chelona Toxin, a diphtheria toxin homolog, from Austwickia chelonae

• PDB DOI: https://doi.org/10.2210/pdb9BIW/pdb

• Classification: TOXIN
• Organism(s): Austwickia chelonae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-24 Released: 2024-08-07 
• Deposition Author(s): Gill, S.K., Sugiman-Marangos, S.N., Melnyk, R.A.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

A diphtheria toxin-like intracellular delivery platform that evades pre-existing antidrug antibodies

Gill, S.K., Sugiman-Marangos, S.N., Beilhartz, G., Mei, E., Taipale, M., Melnyk, R.A.

(null) EMBO Mol Med 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 116.11 kDa 
• Atom Count: 8,218 
• Modeled Residue Count: 1,055 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chelona Toxin	A, B	540	Austwickia chelonae	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.236	α = 90
b = 138.835	β = 90
c = 152.109	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Gill, S.K., Sugiman-Marangos, S.N., Melnyk, R.A.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary