› 4g6r

X-ray diffraction
2.83Å resolution

Minimal Hairpin Ribozyme in the Transition State with G8I Variation

Released:
DOI: 10.2210/pdb4g6r/pdb
PDB entry 4g6r coloured by chain, front view.
PDB entry 4g6r coloured by chain, side view.
PDB entry 4g6r 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196809 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 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 Ribozyme strand Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.96 KDa
Source organism: Synthetic construct
Expression system: Not provided
Loop B Ribozyme Strand Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Synthetic construct
Expression system: Not provided
Loop B S-turn strand Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.99 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand MG 1 x MG
1 modified residue:
Ligand 3DA 1 x 3DA

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P6122
Unit cell:
a: 93.127Å b: 93.127Å c: 128.867Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.176 0.22
Expression system: Not provided

Quick links

Citations

2 review citations

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

1 mention without citation

VfoldMCPX: predicting multistrand RNA complexes.
Zhang et al. (2022)