› 2r6o

X-ray diffraction
1.8Å resolution

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans

Released:
DOI: 10.2210/pdb2r6o/pdb
PDB entry 2r6o coloured by chain, front view.
PDB entry 2r6o coloured by chain, side view.
PDB entry 2r6o coloured by chain, top view.
Source organism: Thiobacillus denitrificans ATCC 25259
Primary publication:
Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin MY, Savchenko A, Yakunin AF
J Mol Biol 402 524-38 (2010)
PMID: 20691189

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174783 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains) Chains: A, B
Molecule details ›
Chains: A, B
Length: 294 amino acids
Theoretical weight: 32.88 KDa
Source organism: Thiobacillus denitrificans ATCC 25259
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3SJE6 (Residues: 487-758; Coverage: 37%)
Gene name: Tbd_1265
Sequence domains: EAL domain
Structure domains: EAL domain

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand CL 3 x CL
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P212121
Unit cell:
a: 50.051Å b: 63.141Å c: 173.282Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.218
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Cyclic di-GMP: the first 25 years of a universal bacterial second messenger.
Römling et al. (2013)
12 more

13 mentions without citation

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms.
He et al. (2020)
12 more