5DIM | pdb_00005dim

Mutant toxin in 'native' space group

• PDB DOI: https://doi.org/10.2210/pdb5DIM/pdb

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


• Deposited: 2015-09-01 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: 3.32 Å
• R-Value Free: 
  0.297 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Structure of mutant toxin at 3.32 Angstrom resolution

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

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)

Macromolecule Content 

• Total Structure Weight: 53.01 kDa 
• Atom Count: 3,692 
• Modeled Residue Count: 465 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Perfringolysin O	A	472	Clostridium perfringens str. 13	Mutation(s): 1  Gene Names: pfo, pfoA, pfoR, CPE0163 Membrane Entity: Yes
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	B [auth A]	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: 3.32 Å
• R-Value Free:  0.297 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.951	α = 90
b = 207.332	β = 90
c = 212.442	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
MOLREP	phasing

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