› 7d82

X-ray diffraction
2.49Å resolution

Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+

Released:
DOI: 10.2210/pdb7d82/pdb
Model geometry
Fit model/data
PDB entry 7d82 coloured by chain, front view.
PDB entry 7d82 coloured by chain, side view.
PDB entry 7d82 coloured by chain, top view.
Source organism: Acidobacteriaceae bacterium KBS 83
Primary publication:
Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.
Chen H, Egger M, Xu X, Flemmich L, Krasheninina O, Sun A, Micura R, Ren A
OpenAccess logo Nucleic Acids Res 48 12394-12406 (2020)
PMID: 33170270

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-303357 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
832GAAA (50-MER) Chain: A
Molecule details ›
Chain: A
Length: 50 nucleotides
Theoretical weight: 16.1 KDa
Source organism: Acidobacteriaceae bacterium KBS 83
Expression system: in vitro transcription vector pT7-TP(deltai)
Sequence domains: nadA riboswitch

Ligands and Environments

3 bound ligands:
Ligand MN 7 x MN
Ligand NAD 1 x NAD
Ligand MG 7 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P3221
Unit cell:
a: 75.916Å b: 75.916Å c: 50.289Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.221 0.271
Expression system: in vitro transcription vector pT7-TP(deltai)

Quick links

Citations

4 review citations

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

2 mentions without citation

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.
Chen et al. (2020)
1 more