› 6zi1

X-ray diffraction
2.2Å resolution

Crystal structure of the isolated H. influenzae VapD toxin (D7N mutant)

Released:
DOI: 10.2210/pdb6zi1/pdb
PDB entry 6zi1 coloured by chain, front view.
PDB entry 6zi1 coloured by chain, side view.
PDB entry 6zi1 coloured by chain, top view.
Source organism: Haemophilus influenzae 86-028NP
Primary publication:
Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System.
Bertelsen MB, Senissar M, Nielsen MH, Bisiak F, Cunha MV, Molinaro AL, Daines DA, Brodersen DE
Structure 29 139-150.e3 (2021)
PMID: 33096014

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175729 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endoribonuclease VapD Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
Length: 102 amino acids
Theoretical weight: 11.87 KDa
Source organism: Haemophilus influenzae 86-028NP
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q4QN95 (Residues: 1-92; Coverage: 100%)
Gene names: NTHI0577, vapD
Sequence domains: CRISPR associated protein Cas2

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P321
Unit cell:
a: 84.38Å b: 84.38Å c: 49.48Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.214 0.267
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Biology and evolution of bacterial toxin-antitoxin systems.
Jurėnas et al. (2022)
3 more

1 mention without citation

Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System.
Bertelsen et al. (2021)