› 488d

X-ray diffraction
3.1Å resolution

CATALYTIC RNA ENZYME-PRODUCT COMPLEX

Released:
DOI: 10.2210/pdb488d/pdb
PDB entry 488d coloured by chain, front view.
PDB entry 488d coloured by chain, side view.
PDB entry 488d coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.
Murray JB, Szöke H, Szöke A, Scott WG
Mol Cell 5 279-87 (2000)
PMID: 10882069

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-196783 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 distinct):
RNA RIBOZYME STRAND Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 5.17 KDa
Source organism: Synthetic construct
Expression system: Not provided
FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.51 KDa
Source organism: Synthetic construct
Expression system: Not provided
SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE Chain: C
Molecule details ›
Chain: C
Length: 5 nucleotides
Theoretical weight: 1.53 KDa
Source organism: Synthetic construct
Expression system: Not provided
UNCLEAVED RNA SUBSTRATE Chain: D
Molecule details ›
Chain: D
Length: 25 nucleotides
Theoretical weight: 8.02 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CD 8 x CD
1 modified residue:
Ligand CCC 1 x CCC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P3121
Unit cell:
a: 65.503Å b: 65.503Å c: 136.484Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.258 0.258 0.301
Expression system: Not provided

Quick links

Citations

16 review citations

The chemical repertoire of natural ribozymes.
Doudna et al. (2002)
15 more