› 4xj4

X-ray diffraction
1.6Å resolution

Crystal structure of Vibrio cholerae DncV 3'-deoxy ATP bound form

Released:
DOI: 10.2210/pdb4xj4/pdb
PDB entry 4xj4 coloured by chain, front view.
PDB entry 4xj4 coloured by chain, side view.
PDB entry 4xj4 coloured by chain, top view.
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Primary publication:
Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase.
Kato K, Ishii R, Hirano S, Ishitani R, Nureki O
Structure 23 843-850 (2015)
PMID: 25865248

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192139 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclic GMP-AMP synthase Chain: A
Molecule details ›
Chain: A
Length: 389 amino acids
Theoretical weight: 44.31 KDa
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KVG7 (Residues: 1-215, 242-412; Coverage: 89%)
Gene names: VC_0179, dncV
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand EDO 5 x EDO
Ligand 3AT 2 x 3AT
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 118.09Å b: 51.3Å c: 71.54Å
α: 90° β: 93.85° γ: 90°
R-values:
R R work R free
0.173 0.172 0.2
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Cyclic di-GMP: second messenger extraordinaire.
Jenal et al. (2017)
2 more

1 mention without citation

Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems.
Millman et al. (2020)