› 2elg

X-ray diffraction
1Å resolution

The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10 degree celsius

Released:
DOI: 10.2210/pdb2elg/pdb
PDB entry 2elg coloured by chain, front view.
PDB entry 2elg coloured by chain, side view.
PDB entry 2elg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The rare crystallographic structure of d(CGCGCG)(2): the natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C.
Ohishi H, Tozuka Y, Da-Yang Z, Ishida T, Nakatani K
Biochem Biophys Res Commun 358 24-8 (2007)
PMID: 17467661

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115207 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SPD 1 x SPD
Ligand MG 3 x MG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P212121
Unit cell:
a: 17.847Å b: 30.988Å c: 44.022Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.253 0.232 0.247
Expression system: Not provided

Quick links

Citations

1 review citation

Endogenous polyamine function--the RNA perspective.
Lightfoot et al. (2014)
4 other articles

7 mentions without citation

Towards automated crystallographic structure refinement with phenix.refine.
Afonine et al. (2012)
6 more