› 4lx5

X-ray diffraction
2.13Å resolution

X-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)

Released:
DOI: 10.2210/pdb4lx5/pdb
PDB entry 4lx5 coloured by chain, front view.
PDB entry 4lx5 coloured by chain, side view.
PDB entry 4lx5 coloured by chain, top view.
Source organism: Vibrio vulnificus
Primary publication:
Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.
Robinson CJ, Vincent HA, Wu MC, Lowe PT, Dunstan MS, Leys D, Micklefield J
J Am Chem Soc 136 10615-24 (2014)
PMID: 24971878

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-195852 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
Mutated adenine riboswitch aptamer Chain: A
Molecule details ›
Chain: A
Length: 71 nucleotides
Theoretical weight: 22.69 KDa
Source organism: Vibrio vulnificus
Expression system: Not provided
Sequence domains: Purine riboswitch

Ligands and Environments

2 bound ligands:
Ligand 29G 1 x 29G
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21212
Unit cell:
a: 49.05Å b: 149.71Å c: 24.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.199 0.257
Expression system: Not provided

Quick links

Citations

11 review citations

New tools for recombinant protein production in Escherichia coli: A 5-year update.
Rosano et al. (2019)
10 more

3 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)
2 more