4R04 | pdb_00004r04

Clostridium difficile Toxin A (TcdA)

PDB DOI: https://doi.org/10.2210/pdb4R04/pdb

Classification: TRANSFERASE
Organism(s): Clostridioides difficile
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2014-07-29 Released: 2016-01-06
Deposition Author(s): Lacy, D.B., Spiller, B.W., Rutherford, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Glucosyl Transferase Structure

Lacy, D.B., Spiller, B.W., Rutherford, S.A.

(2016) Nat Microbiol

Macromolecule Content

Total Structure Weight: 209.91 kDa
Atom Count: 14,410
Modeled Residue Count: 1,793
Deposited Residue Count: 1,838
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin A	A	1,838	Clostridioides difficile	Mutation(s): 0 Gene Names: Clostridium difficile, tcdA, toxA EC: 3.4.22 Membrane Entity: Yes
UniProt
Find proteins for P16154 (Clostridioides difficile) Explore P16154 Go to UniProtKB: P16154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16154
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 303.49	α = 90
b = 124.54	β = 97.5
c = 75.95	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-01-06

Deposition Author(s):

Rutherford, S.A.

Revision History (Full details and data files)

Version 1.0: 2016-01-06
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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 R01GM157729.