6X6V

Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb6X6V/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile in complex with NADPH

Pozharski, E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 201.13 kDa 
• Atom Count: 14,229 
• Modelled Residue Count: 1,664 
• Deposited Residue Count: 1,716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdtA	A, B, C, D	429	Clostridioides difficile	Mutation(s): 0  Gene Names: cdtA
UniProt
Find proteins for Q9KH42 (Clostridioides difficile) Explore Q9KH42  Go to UniProtKB:  Q9KH42

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.77	α = 98.8
b = 101.1	β = 112.36
c = 104.33	γ = 106.72

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