› 1g8v

X-ray diffraction
1.8Å resolution

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA

Released:
DOI: 10.2210/pdb1g8v/pdb
PDB entry 1g8v coloured by chain, front view.
PDB entry 1g8v coloured by chain, side view.
PDB entry 1g8v coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?
Tsunoda M, Karino N, Ueno Y, Matsuda A, Takenaka A
Acta Crystallogr D Biol Crystallogr 57 345-8 (2001)
PMID: 11173500

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-113857 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*CP*GP*CP*GP*AP*AP*TP*(UFR)P*CP*GP*CP*G)-3' 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

No bound ligands
1 modified residue:
Ligand UFR 2 x UFR

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6B
Spacegroup: P212121
Unit cell:
a: 25.3Å b: 41.7Å c: 66Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.239
Expression system: Not provided

Quick links

Citations

2 review citations

Structural characterization of the Fpg family of DNA glycosylases.
Zharkov et al. (2003)
1 more

2 mentions without citation

Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil.
Tsunoda et al. (2010)
1 more