› 3zd4

X-ray diffraction
2.2Å resolution

Full-Length Hammerhead Ribozyme with G12A substitution at the general base position

Released:
DOI: 10.2210/pdb3zd4/pdb
PDB entry 3zd4 coloured by chain, front view.
PDB entry 3zd4 coloured by chain, side view.
PDB entry 3zd4 coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.
Schultz EP, Vasquez EE, Scott WG
Acta Crystallogr D Biol Crystallogr 70 2256-63 (2014)
PMID: 25195740

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196755 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
HAMMERHEAD RIBOZYME, ENZYME STRAND Chain: A
Molecule details ›
Chain: A
Length: 43 nucleotides
Theoretical weight: 13.93 KDa
Source organism: synthetic construct
Expression system: Not provided
HAMMERHEAD RIBOZYME, SUBSTRATE STRAND Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.33 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand GDP 1 x GDP
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2
Unit cell:
a: 50.14Å b: 68.45Å c: 60.22Å
α: 90° β: 112.56° γ: 90°
R-values:
R R work R free
0.188 0.182 0.236
Expression system: Not provided

Quick links

Citations

4 citation in other articles

Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.
Mir et al. (2016)
3 more

1 mention without citation

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.
Schultz et al. (2014)