› 5l6l

X-ray diffraction
2.7Å resolution

Structure of Caulobacter crescentus VapBC1 bound to operator DNA

Released:
DOI: 10.2210/pdb5l6l/pdb
PDB entry 5l6l coloured by chain, front view.
PDB entry 5l6l coloured by chain, side view.
PDB entry 5l6l 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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118980 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
VapB family protein Chains: A, D, E, H
Molecule details ›
Chains: A, D, E, H
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, F, G
Molecule details ›
Chains: B, C, F, G
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
DNA (27-MER) Chain: M
Molecule details ›
Chain: M
Length: 27 nucleotides
Theoretical weight: 8.2 KDa
DNA (27-MER) Chain: N
Molecule details ›
Chain: N
Length: 27 nucleotides
Theoretical weight: 8.39 KDa

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: C2221
Unit cell:
a: 110.18Å b: 144.16Å c: 160.54Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.178 0.24
Expression system: Escherichia coli B

Quick links

Citations

2 review citations

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

1 mention without citation

Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.
Bendtsen et al. (2017)