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.

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile

Pozharski, E.

To be published.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KH42
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.