6X6X | pdb_00006x6x

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

• PDB DOI: https://doi.org/10.2210/pdb6X6X/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: 1.71 Å
• R-Value Free: 
  0.226 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

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

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.

Macromolecule Content 

• Total Structure Weight: 97.16 kDa 
• Atom Count: 7,291 
• Modeled Residue Count: 833 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyltransferase	A, B	420	Clostridioides difficile	Mutation(s): 0  Gene Names: cdtA EC: 2.4.2
UniProt
Find proteins for Q9KH42 (Clostridioides difficile) Explore Q9KH42  Go to UniProtKB:  Q9KH42

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTG (Subject of Investigation/LOI)	E [auth A]	N-(2-chlorophenyl)-N'-[(furan-2-yl)methyl]thiourea C12 H11 Cl N2 O S QDQNQQPXAIJIJW-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.226 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.956	α = 90
b = 97.706	β = 90
c = 106.366	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