› 6dmd

X-ray diffraction
2.65Å resolution

ppGpp Riboswitch bound to ppGpp, manganese chloride structure

Released:
DOI: 10.2210/pdb6dmd/pdb
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PDB entry 6dmd coloured by chain, front view.
PDB entry 6dmd coloured by chain, side view.
PDB entry 6dmd coloured by chain, top view.
Source organism: Sulfobacillus acidophilus DSM 10332
Primary publication:
ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.
Peselis A, Serganov A
OpenAccess logo Nat Chem Biol 14 887-894 (2018)
PMID: 30120360

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197063 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
ppGpp Riboswitch Chains: A, B
Molecule details ›
Chains: A, B
Length: 102 nucleotides
Theoretical weight: 33.32 KDa
Source organism: Sulfobacillus acidophilus DSM 10332
Expression system: in vitro transcription vector pT7-TP(deltai)

Ligands and Environments

5 bound ligands:
Ligand G4P 2 x G4P
Ligand MN 10 x MN
Ligand NA 8 x NA
Ligand MG 8 x MG
Ligand K 1 x K
2 modified residues:
Ligand GTP 2 x GTP
Ligand CCC 2 x CCC

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS-II BEAMLINE 17-ID-2
Spacegroup: P21
Unit cell:
a: 78.741Å b: 49.595Å c: 79.365Å
α: 90° β: 97.29° γ: 90°
R-values:
R R work R free
0.22 0.217 0.272
Expression system: in vitro transcription vector pT7-TP(deltai)

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Citations

6 review citations

Discovering riboswitches: the past and the future.
Kavita et al. (2023)
5 more

2 mentions without citation

ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.
Peselis et al. (2018)
1 more

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