› 1zfv

X-ray diffraction
2.4Å resolution

The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site

Released:
DOI: 10.2210/pdb1zfv/pdb
PDB entry 1zfv coloured by chain, front view.
PDB entry 1zfv coloured by chain, side view.
PDB entry 1zfv coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.
Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE
Biochemistry 45 686-700 (2006)
PMID: 16411744

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-196287 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 distinct):
5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3' Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 4.05 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-R(*CP*GP*GP*UP*GP*AP*AP*AP*AP*GP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' 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 NCO 1 x NCO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P6122
Unit cell:
a: 93.51Å b: 93.51Å c: 124.55Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.243 0.243 0.253
Expression system: Not provided

Quick links

Citations

11 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
10 more

3 mentions without citation

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.
Salter et al. (2006)
2 more