› 1ub8

X-ray diffraction
1.6Å resolution

Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue

Released:
DOI: 10.2210/pdb1ub8/pdb
PDB entry 1ub8 coloured by chain, front view.
PDB entry 1ub8 coloured by chain, side view.
PDB entry 1ub8 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.
Sunami T, Kondo J, Hirao I, Watanabe K, Miura K, Takénaka A
Acta Crystallogr D Biol Crystallogr 60 422-31 (2004)
PMID: 14993665

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-114695 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*GP*CP*GP*AP*AP*GP*C)-3' Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 7 nucleotides
Theoretical weight: 2.15 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NCO 9 x NCO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: P212121
Unit cell:
a: 48.675Å b: 48.856Å c: 63.761Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.194 0.232
Expression system: Not provided

Quick links

Citations

3 review citations

The Halogen Bond.
Cavallo et al. (2016)
2 more

1 mention without citation

DNA conformations and their sequence preferences.
Svozil et al. (2008)