› 1sr4

X-ray diffraction
2Å resolution

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

Released:
DOI: 10.2210/pdb1sr4/pdb
PDB entry 1sr4 coloured by chain, front view.
PDB entry 1sr4 coloured by chain, side view.
PDB entry 1sr4 coloured by chain, top view.
Source organism: [Haemophilus] ducreyi
Primary publication:
Assembly and function of a bacterial genotoxin.
Nesić D, Hsu Y, Stebbins CE
Nature 429 429-33 (2004)
PMID: 15164065

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-126517 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cytolethal distending toxin subunit A Chain: A
Molecule details ›
Chain: A
Length: 206 amino acids
Theoretical weight: 22.87 KDa
Source organism: [Haemophilus] ducreyi
Expression system: Escherichia coli
UniProt:
  • Canonical: O06522 (Residues: 18-223; Coverage: 99%)
Gene names: HD_0902, cdtA
Sequence domains: Cytolethal distending toxin A/C domain
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Endonuclease/exonuclease/phosphatase domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 261 amino acids
Theoretical weight: 28.99 KDa
Source organism: [Haemophilus] ducreyi
Expression system: Escherichia coli
UniProt:
  • Canonical: O06523 (Residues: 23-283; Coverage: 100%)
Gene names: RZ57_03560, cdtB
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
Cytolethal distending toxin protein C Chain: C
Molecule details ›
Chain: C
Length: 166 amino acids
Theoretical weight: 18.38 KDa
Source organism: [Haemophilus] ducreyi
Expression system: Escherichia coli
UniProt:
  • Canonical: O06524 (Residues: 21-186; Coverage: 100%)
Gene names: RZ57_03565, cdtC
Sequence domains: Cytolethal distending toxin A/C domain
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)

Ligands and Environments

1 bound ligand:
Ligand BR 26 x BR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9A
Spacegroup: P212121
Unit cell:
a: 71.652Å b: 75.653Å c: 121.637Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.182 0.214
Expression system: Escherichia coli

Quick links

Citations

66 review citations

The microbiome and cancer.
Schwabe et al. (2013)
65 more

23 mentions without citation

Bacterial Genotoxins: Merging the DNA Damage Response into Infection Biology.
Grasso et al. (2015)
22 more