› 5k8j

X-ray diffraction
1.6Å resolution

Structure of Caulobacter crescentus VapBC1 (apo form)

Released:
DOI: 10.2210/pdb5k8j/pdb
PDB entry 5k8j coloured by chain, front view.
PDB entry 5k8j coloured by chain, side view.
PDB entry 5k8j coloured by chain, top view.
Source organism: Caulobacter vibrioides CB15
Primary publication:
Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.
Bendtsen KL, Xu K, Luckmann M, Winther KS, Shah SA, Pedersen CNS, Brodersen DE
Nucleic Acids Res 45 2875-2886 (2017)
PMID: 27998932

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189522 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
VapB family protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 85 amino acids
Theoretical weight: 9.55 KDa
Source organism: Caulobacter vibrioides CB15
Expression system: Escherichia coli B
UniProt:
  • Canonical: Q9AC34 (Residues: 2-79; Coverage: 99%)
Gene name: CC_0032
Ribonuclease VapC Chains: B, C
Molecule details ›
Chains: B, C
Length: 128 amino acids
Theoretical weight: 14.29 KDa
Source organism: Caulobacter vibrioides CB15
Expression system: Escherichia coli B
UniProt:
  • Canonical: Q9AC35 (Residues: 1-128; Coverage: 100%)
Gene names: CC_0031, vapC
Sequence domains: PIN domain
Structure domains: 5'-nuclease

Ligands and Environments

1 bound ligand:
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: P3121
Unit cell:
a: 86.29Å b: 86.29Å c: 113.82Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.158 0.158 0.168
Expression system: Escherichia coli B

Quick links

Citations

6 citation in other articles

Mechanism of regulation and neutralization of the AtaR-AtaT toxin-antitoxin system.
Jurėnas et al. (2019)
5 more

2 mentions without citation

Structural conservation of the PIN domain active site across all domains of life.
Senissar et al. (2017)
1 more