› 1f6c

X-ray diffraction
2.7Å resolution

CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE

Released:
DOI: 10.2210/pdb1f6c/pdb
PDB entry 1f6c coloured by chain, front view.
PDB entry 1f6c coloured by chain, side view.
PDB entry 1f6c coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
Vargason JM, Eichman BF, Ho PS
Nat Struct Biol 7 758-61 (2000)
PMID: 10966645

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-113794 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*GP*GP*CP*GP*CP*C)-3') Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SPM 2 x SPM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P41212
Unit cell:
a: 71.5Å b: 71.5Å c: 59.63Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.226 0.288
Expression system: Not provided

Quick links

Citations

6 review citations

Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development.
Patra et al. (2008)
5 more

2 mentions without citation

The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions.
Eichman et al. (2002)
1 more