› 4gju

X-ray diffraction
1.41Å resolution

5-Methylcytosine modified DNA oligomer

Released:
DOI: 10.2210/pdb4gju/pdb
PDB entry 4gju coloured by chain, front view.
PDB entry 4gju coloured by chain, side view.
PDB entry 4gju coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Renciuk D, Blacque O, Vorlickova M, Spingler B
Nucleic Acids Res 41 9891-900 (2013)
PMID: 23963698

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-117547 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5-Methylcytosine modified DNA oligomer Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 25.495Å b: 40.4Å c: 65.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.215
Expression system: Not provided

Quick links

Citations

8 review citations

Hydroxymethylation of DNA: an epigenetic marker.
Richa et al. (2014)
7 more

4 mentions without citation

Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Renciuk et al. (2013)
3 more