› 2npy

X-ray diffraction
2.65Å resolution

Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1

Released:
DOI: 10.2210/pdb2npy/pdb
PDB entry 2npy coloured by chain, front view.
PDB entry 2npy coloured by chain, side view.
PDB entry 2npy coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
MacElrevey C, Spitale RC, Krucinska J, Wedekind JE
Acta Crystallogr D Biol Crystallogr 63 812-25 (2007)
PMID: 17582172

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-196537 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 distinct):
5'-R(*UP*CP*CP*CP*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-3' Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 4.03 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.97 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 NCO 1 x NCO
Ligand S9L 1 x S9L
1 modified residue:
Ligand 2AU 1 x 2AU

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P6122
Unit cell:
a: 94.29Å b: 94.29Å c: 131.11Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.196 0.223
Expression system: Not provided

Quick links

Citations

1 review citation

Exploring ribozyme conformational changes with X-ray crystallography.
Spitale et al. (2009)
7 other articles

1 mention without citation

A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
MacElrevey et al. (2007)