6X6W

Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb6X6W/pdb

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


• Deposited: 2020-05-29 Released: 2021-07-28 
• Deposition Author(s): Pozharski, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile

Pozharski, E.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 48.28 kDa 
• Atom Count: 3,667 
• Modelled Residue Count: 410 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyltransferase	A [auth B]	420	Clostridioides difficile	Mutation(s): 0  Gene Names: cdtA
UniProt
Find proteins for Q9KH42 (Clostridioides difficile) Explore Q9KH42  Go to UniProtKB:  Q9KH42

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.24	α = 90
b = 44.47	β = 116.96
c = 78.39	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Pozharski, E.

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description