› 3n3t

X-ray diffraction
2.35Å resolution

Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

Released:
DOI: 10.2210/pdb3n3t/pdb
PDB entry 3n3t coloured by chain, front view.
PDB entry 3n3t coloured by chain, side view.
PDB entry 3n3t 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 BL21(DE3)
UniProt:
  • Canonical: Q3SJE6 (Residues: 487-758; Coverage: 37%)
Gene name: Tbd_1265
Sequence domains: EAL domain
Structure domains: EAL domain

Ligands and Environments

3 bound ligands:
Ligand C2E 2 x C2E
Ligand MG 4 x MG
Ligand CL 1 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: 51.56Å b: 63.201Å c: 173.987Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.184 0.254
Expression system: Escherichia coli BL21(DE3)

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Citations

12 review citations

Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis.
Kalia et al. (2013)
11 more

8 mentions without citation

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