› 3zvk

X-ray diffraction
2.5Å resolution

Crystal structure of VapBC2 from Rickettsia felis bound to a DNA fragment from their promoter

Released:
DOI: 10.2210/pdb3zvk/pdb
PDB entry 3zvk coloured by chain, front view.
PDB entry 3zvk coloured by chain, side view.
PDB entry 3zvk coloured by chain, top view.
Source organism: Rickettsia felis
Primary publication:
Crystal structure of the DNA-bound VapBC2 antitoxin/toxin pair from Rickettsia felis.
Maté MJ, Vincentelli R, Foos N, Raoult D, Cambillau C, Ortiz-Lombardía M
Nucleic Acids Res 40 3245-58 (2012)
PMID: 22140099

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117123 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Ribonuclease VapC2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 134 amino acids
Theoretical weight: 15.32 KDa
Source organism: Rickettsia felis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q4UNB2 (Residues: 1-134; Coverage: 100%)
Gene names: RF_0095, vapC2
Sequence domains: PIN domain
Structure domains: 5'-nuclease
Antitoxin VapB2 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 78 amino acids
Theoretical weight: 9.02 KDa
Source organism: Rickettsia felis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q4UNB3 (Residues: 1-78; Coverage: 100%)
Gene names: RF_0094, vapB2
DNA Chain: X
Molecule details ›
Chain: X
Length: 26 nucleotides
Theoretical weight: 8.02 KDa
DNA Chain: Y
Molecule details ›
Chain: Y
Length: 26 nucleotides
Theoretical weight: 7.94 KDa

Ligands and Environments

1 bound ligand:
Ligand MES 4 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1, ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 80.78Å b: 92.333Å c: 150.495Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.217
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Toxin-antitoxin systems are ubiquitous and versatile modulators of prokaryotic cell fate.
Schuster et al. (2013)
7 more

11 mentions without citation

Structure, Biology, and Therapeutic Application of Toxin-Antitoxin Systems in Pathogenic Bacteria.
Lee et al. (2016)
10 more