› 4glc

X-ray diffraction
1.83Å resolution

DNA dodecamer containing 5-hydroxymethyl-cytosine

Released:
DOI: 10.2210/pdb4glc/pdb
PDB entry 4glc coloured by chain, front view.
PDB entry 4glc coloured by chain, side view.
PDB entry 4glc 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-117548 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5HC 2 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 24.513Å b: 41.602Å c: 66.044Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.233 0.306
Expression system: Not provided

Quick links

Citations

8 review citations

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

576 mentions without citation

Update of the LIPID MAPS comprehensive classification system for lipids.
Fahy et al. (2009)
575 more