› 8ruj

X-ray diffraction
3.12Å resolution

Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking

Released:
DOI: 10.2210/pdb8ruj/pdb
PDB entry 8ruj coloured by chain, front view.
PDB entry 8ruj coloured by chain, side view.
PDB entry 8ruj coloured by chain, top view.
Source organism: Oceanobacillus iheyensis
Primary publication:
Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.
Silvestri I, Manigrasso J, Andreani A, Brindani N, Mas C, Reiser JB, Vidossich P, Martino G, McCarthy AA, De Vivo M, Marcia M
Nat Commun 15 4980 (2024)
PMID: 38898052

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-195918 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
Domains 1-5 Chain: A
Molecule details ›
Chain: A
Length: 391 nucleotides
Theoretical weight: 126.96 KDa
Source organism: Oceanobacillus iheyensis
Expression system: Not provided
Sequence domains:
  • Group II catalytic intron D1-D4-3
  • Group II catalytic intron D1-D4-1

    • Ligands and Environments

    3 bound ligands:
    Ligand VTR 1 x VTR
    Ligand MG 21 x MG
    Ligand K 18 x K
    No modified residues

    Experiments and Validation Details

    Entry percentile scores
    X-ray source: ESRF BEAMLINE ID30B
    Spacegroup: P212121
    Unit cell:
    a: 89.57Å b: 95.098Å c: 227.801Å
    α: 90° β: 90° γ: 90°
    R-values:
    R R work R free
    0.198 0.196 0.236
    Expression system: Not provided

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