› 4g6s

X-ray diffraction
2.84Å resolution

Minimal Hairpin Ribozyme in the Transition State with A38P Variation

Released:
DOI: 10.2210/pdb4g6s/pdb
PDB entry 4g6s coloured by chain, front view.
PDB entry 4g6s coloured by chain, side view.
PDB entry 4g6s coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.
Liberman JA, Guo M, Jenkins JL, Krucinska J, Chen Y, Carey PR, Wedekind JE
J Am Chem Soc 134 16933-6 (2012)
PMID: 22989273

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-196810 (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: 4.04 KDa
Source organism: Synthetic construct
Expression system: Not provided
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 of the Ribozyme Strand Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.98 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 3DA 1 x 3DA
Ligand P5P 1 x P5P

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P6122
Unit cell:
a: 93.966Å b: 93.966Å c: 134.171Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.222
Expression system: Not provided

Quick links

Citations

2 review citations

Nucleic acid catalysis: metals, nucleobases, and other cofactors.
Ward et al. (2014)
1 more