2QJ6 | pdb_00002qj6

Crystal structure analysis of a 14 repeat C-terminal fragment of toxin TcdA in Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb2QJ6/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-06 Released: 2008-07-15 
• Deposition Author(s): Albesa-Jove, D., Bertrand, T., Carpenter, L., Lim, J., Brown, K.A., Fairweather, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Solution and crystal structures of the cell binding domain of toxins TcdA and TcdB from Clostridium difficile

Albesa-Jove, D., Bertrand, T., Carpenter, L., Lim, J., Martinez, E., Zhang, J., Dmitri, I., Brown, K.A., Fairweather, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.48 kDa 
• Atom Count: 5,227 
• Modeled Residue Count: 634 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin A	A, B	332	N/A	Mutation(s): 0  Gene Names: toxA, tcdA EC: 3.4.22
UniProt
Find proteins for P16154 (Clostridioides difficile) Explore P16154  Go to UniProtKB:  P16154

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.05	α = 90
b = 199.68	β = 90.01
c = 58.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Albesa-Jove, D., Bertrand, T., Carpenter, L., Lim, J., Brown, K.A., Fairweather, N.

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description