› 4xj6

X-ray diffraction
2.31Å resolution

Crystal structure of Escherichia coli DncV 3'-deoxy GTP bound form

Released:
DOI: 10.2210/pdb4xj6/pdb
PDB entry 4xj6 coloured by chain, front view.
PDB entry 4xj6 coloured by chain, side view.
PDB entry 4xj6 coloured by chain, top view.
Source organism: Escherichia coli
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:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180527 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclic GMP-AMP synthase Chain: A
Molecule details ›
Chain: A
Length: 407 amino acids
Theoretical weight: 46.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6XGD8 (Residues: 1-407; Coverage: 94%)
Gene names: DU321_04130, dncV
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand GH3 2 x GH3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: C2
Unit cell:
a: 136.07Å b: 46.3Å c: 62.56Å
α: 90° β: 110.61° γ: 90°
R-values:
R R work R free
0.191 0.189 0.234
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)