6X41 | pdb_00006x41

Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb6X41/pdb

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


• Deposited: 2020-05-21 Released: 2021-12-15 
• Deposition Author(s): Pozharski, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 
  0.246 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

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.

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: 99.26 kDa 
• Atom Count: 6,998 
• Modeled Residue Count: 834 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdtA	A, B	429	Clostridioides difficile	Mutation(s): 0  Gene Names: cdtA
UniProt
Find proteins for F5B5W8 (Clostridioides difficile) Explore F5B5W8  Go to UniProtKB:  F5B5W8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.246 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.116	α = 90
b = 114.116	β = 90
c = 179.128	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: 2021-12-15 
Deposition Author(s): Pozharski, E.

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description