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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.246 (Depositor), 0.267 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F5B5W8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.246 (Depositor), 0.267 (DCC)
R-Value Work: 0.202 (Depositor)
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

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Entry History

Deposition Data

Released Date: 2021-12-15

Deposition Author(s):

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.