5DHL

Crystal structure of Toxin, mutant N197W

• PDB DOI: https://doi.org/10.2210/pdb5DHL/pdb

• Classification: TOXIN
• Organism(s): Clostridium perfringens str. 13
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-31 Released: 2016-11-09 
• Deposition Author(s): Parker, M.W., Gorman, M.A., Lawrence, S.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.239 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Structure of mutant toxin

Parker, M.W., Gorman, M.A., Lawrence, S.L., Morton, C.J.

To be published.

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: 106.03 kDa 
• Atom Count: 7,511 
• Modelled Residue Count: 934 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Perfringolysin O	A, B	472	Clostridium perfringens str. 13	Mutation(s): 1  Gene Names: pfo, pfoA, pfoR, CPE0163
UniProt
Find proteins for P0C2E9 (Clostridium perfringens (strain 13 / Type A)) Explore P0C2E9  Go to UniProtKB:  P0C2E9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.239 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.629	α = 90
b = 212.398	β = 97.17
c = 46.958	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Parker, M.W., Gorman, M.A., Lawrence, S.L.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description