6X6R | pdb_00006x6r

Crystal structure of C.difficile ribosyltransferase CDTa in complex with pCl-phenylthioDADMeImmA

• PDB DOI: https://doi.org/10.2210/pdb6X6R/pdb

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


• Deposited: 2020-05-29 Released: 2021-10-13 
• Deposition Author(s): Pozharski, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of C.difficile ribosyltransferase CDTa in complex with pCl-phenylthioDADMeImmA

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: 97.89 kDa 
• Atom Count: 7,449 
• Modeled Residue Count: 831 
• 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
UniProt
Find proteins for F5B5W8 (Clostridioides difficile) Explore F5B5W8  Go to UniProtKB:  F5B5W8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	D [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
4CT (Subject of Investigation/LOI)	C [auth A], E [auth B]	(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol C18 H20 Cl N5 O S MZZBHZOHYGEGEE-DOMZBBRYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.442	α = 90
b = 76.066	β = 122.1
c = 100.227	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: 2021-10-13 
Deposition Author(s): Pozharski, E.

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary