› 4fep

X-ray diffraction
1.65Å resolution

Crystal structure of the A24U/U25A/A46G/C74U mutant xpt-pbuX guanine riboswitch aptamer domain in complex with 2,6-diaminopurine

Released:
DOI: 10.2210/pdb4fep/pdb
PDB entry 4fep coloured by chain, front view.
PDB entry 4fep coloured by chain, side view.
PDB entry 4fep coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch.
Stoddard CD, Widmann J, Trausch JJ, Marcano-Velázquez JG, Knight R, Batey RT
J Mol Biol 425 1596-611 (2013)
PMID: 23485418

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-196806 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
A24U/U25A/A46G/C74U mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain Chain: B
Molecule details ›
Chain: B
Length: 67 nucleotides
Theoretical weight: 21.52 KDa
Source organism: Bacillus subtilis
Expression system: Not provided
Sequence domains: Purine riboswitch

Ligands and Environments

2 bound ligands:
Ligand 6AP 1 x 6AP
Ligand NCO 9 x NCO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2
Unit cell:
a: 133.071Å b: 35.252Å c: 41.855Å
α: 90° β: 91.4° γ: 90°
R-values:
R R work R free
0.179 0.179 0.229
Expression system: Not provided

Quick links

Citations

11 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
10 more

4 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)
3 more