› 2got

X-ray diffraction
2.6Å resolution

Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes

Released:
DOI: 10.2210/pdb2got/pdb
PDB entry 2got coloured by chain, front view.
PDB entry 2got coloured by chain, side view.
PDB entry 2got coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
Kondo J, Sunami T, Takénaka A
Acta Crystallogr D Biol Crystallogr 63 673-81 (2007)
PMID: 17505105

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115307 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*DGP*(CBR)P*DGP*DAP*DAP*DCP*DGP*DC)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 8 nucleotides
Theoretical weight: 2.52 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand CBR 2 x CBR

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: P6122
Unit cell:
a: 26.83Å b: 26.83Å c: 226.325Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.254 0.253 0.269
Expression system: Not provided

Quick links

Citations

1 citations in other articles

Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy.
Smith et al. (2009)