› 3dj2

X-ray diffraction
2.5Å resolution

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Tl+ Soak

Released:
DOI: 10.2210/pdb3dj2/pdb
PDB entry 3dj2 coloured by chain, front view.
PDB entry 3dj2 coloured by chain, side view.
PDB entry 3dj2 coloured by chain, top view.
Source organism: Thermotoga maritima
Primary publication:
Structural insights into amino acid binding and gene control by a lysine riboswitch.
Serganov A, Huang L, Patel DJ
Nature 455 1263-7 (2008)
PMID: 18784651

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-250428 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
RNA (174-MER) Chain: A
Molecule details ›
Chain: A
Length: 174 nucleotides
Theoretical weight: 56.64 KDa
Source organism: Thermotoga maritima
Expression system: Not provided
Sequence domains: Lysine riboswitch aptamer

Ligands and Environments

4 bound ligands:
Ligand NA 8 x NA
Ligand LYS 1 x LYS
Ligand TL 10 x TL
Ligand IPA 1 x IPA
1 modified residue:
Ligand CCC 1 x CCC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 54.086Å b: 78.751Å c: 140.992Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.205 0.251
Expression system: Not provided

Quick links

Citations

49 review citations

A decade of riboswitches.
Serganov et al. (2013)
48 more

5 mentions without citation

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.
Antunes et al. (2017)
4 more