› 2p7f

X-ray diffraction
2.35Å resolution

The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme

Released:
DOI: 10.2210/pdb2p7f/pdb
PDB entry 2p7f coloured by chain, front view.
PDB entry 2p7f coloured by chain, side view.
PDB entry 2p7f coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
Torelli AT, Krucinska J, Wedekind JE
RNA 13 1052-70 (2007)
PMID: 17488874

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-196559 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 distinct):
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: 3.97 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 NCO 2 x NCO
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: 94.1Å b: 94.1Å c: 127.2Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.227 0.252
Expression system: Not provided

Quick links

Citations

7 review citations

Comparative enzymology and structural biology of RNA self-cleavage.
Fedor MJ. (2009)
6 more

7 mentions without citation

Exploring ribozyme conformational changes with X-ray crystallography.
Spitale et al. (2009)
6 more