› 4qkk

X-ray diffraction
1.4Å resolution

Crystal structure of an oligonucleotide containing 5-formylcytosine

Released:
DOI: 10.2210/pdb4qkk/pdb
PDB entry 4qkk coloured by chain, front view.
PDB entry 4qkk coloured by chain, side view.
PDB entry 4qkk coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
5-Formylcytosine alters the structure of the DNA double helix.
Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S
Nat Struct Mol Biol 22 44-49 (2015)
PMID: 25504322

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-118019 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*CP*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 12 nucleotides
Theoretical weight: 3.75 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5FC 3 x 5FC

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P43212
Unit cell:
a: 44.393Å b: 44.393Å c: 46.254Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.141 0.14 0.159
Expression system: Not provided

Quick links

Citations

25 review citations

TET-mediated active DNA demethylation: mechanism, function and beyond.
Wu et al. (2017)
24 more

4 mentions without citation

Are there specific readers of oxidized 5-methylcytosine bases?
Song et al. (2016)
3 more