› 2ygt

X-ray diffraction
2.4Å resolution

Clostridium perfringens delta-toxin

Released:
DOI: 10.2210/pdb2ygt/pdb
PDB entry 2ygt coloured by chain, front view.
PDB entry 2ygt coloured by chain, side view.
PDB entry 2ygt coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
Structural Insights into Clostridium perfringens Delta Toxin Pore Formation.
Huyet J, Naylor CE, Savva CG, Gibert M, Popoff MR, Basak AK
PLoS One 8 e66673 (2013)
PMID: 23805259

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110756 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Leukocidin/Hemolysin toxin domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 298 amino acids
Theoretical weight: 33.63 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B8QGZ7 (Residues: 29-318; Coverage: 100%)
Sequence domains: Leukocidin/Hemolysin toxin family
Structure domains: Leukocidin/porin MspA

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand IMD 1 x IMD
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21212
Unit cell:
a: 112.932Å b: 49.664Å c: 58.477Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Pore-forming toxins: ancient, but never really out of fashion.
Dal Peraro et al. (2016)
2 more

6 mentions without citation

Structural Basis of the Pore-Forming Toxin/Membrane Interaction.
Li et al. (2021)
5 more