› 4qk8

X-ray diffraction
3.05Å resolution

Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch

Released:
DOI: 10.2210/pdb4qk8/pdb
PDB entry 4qk8 coloured by chain, front view.
PDB entry 4qk8 coloured by chain, side view.
PDB entry 4qk8 coloured by chain, top view.
Source organism: Thermoanaerobacter pseudethanolicus
Primary publication:
Structural insights into recognition of c-di-AMP by the ydaO riboswitch.
Gao A, Serganov A
Nat Chem Biol 10 787-92 (2014)
PMID: 25086507

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195880 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
C-di-AMP riboswitch Chain: A
Molecule details ›
Chain: A
Length: 122 nucleotides
Theoretical weight: 39.72 KDa
Source organism: Thermoanaerobacter pseudethanolicus
Expression system: Not provided
Sequence domains: ydaO/yuaA leader

Ligands and Environments

4 bound ligands:
Ligand 2BA 2 x 2BA
Ligand MG 4 x MG
Ligand K 1 x K
Ligand SO4 1 x SO4
2 modified residues:
Ligand GTP 1 x GTP
Ligand 23G 1 x 23G

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P3121
Unit cell:
a: 114.868Å b: 114.868Å c: 114.709Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.181 0.195
Expression system: Not provided

Quick links

Citations

13 review citations

Bacterial Signal Transduction by Cyclic Di-GMP and Other Nucleotide Second Messengers.
Hengge et al. (2016)
12 more

11 mentions without citation

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