› 3b5s

X-ray diffraction
2.25Å resolution

Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'-O-methyl Modification at the Active Site

Released:
DOI: 10.2210/pdb3b5s/pdb
PDB entry 3b5s coloured by chain, front view.
PDB entry 3b5s coloured by chain, side view.
PDB entry 3b5s coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
MacElrevey C, Salter JD, Krucinska J, Wedekind JE
RNA 14 1600-16 (2008)
PMID: 18596253

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196628 (preferred)
Entry contents:
3 distinct RNA molecules
Macromolecules (3 distinct):
Loop A Substrate strand Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Synthetic construct
Expression system: Not provided
29-mer Loop A and Loop B Ribozyme strand Chain: B
Molecule details ›
Chain: B
Length: 30 nucleotides
Theoretical weight: 9.76 KDa
Source organism: Synthetic construct
Expression system: Not provided
Loop B S-turn strand Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 6.01 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand NCO 2 x NCO
2 modified residues:
Ligand A2M 1 x A2M
Ligand N6G 1 x N6G

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P6122
Unit cell:
a: 93.5Å b: 93.5Å c: 133.42Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.223 0.223 0.241
Expression system: Not provided

Quick links

Citations

4 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
3 more

1 mention without citation

Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.
Kailasam et al. (2014)