› 1vro

X-ray diffraction
1.1Å resolution

Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure

Released:
DOI: 10.2210/pdb1vro/pdb
PDB entry 1vro coloured by chain, front view.
PDB entry 1vro coloured by chain, side view.
PDB entry 1vro coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure.
Wilds CJ, Pattanayek R, Pan C, Wawrzak Z, Egli M
J Am Chem Soc 124 14910-6 (2002)
PMID: 12475332

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-114727 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*CP*(GMS)P*CP*GP*CP*G)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 6 nucleotides
Theoretical weight: 1.87 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SPM 1 x SPM
Ligand MG 1 x MG
1 modified residue:
Ligand GMS 2 x GMS

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P212121
Unit cell:
a: 17.778Å b: 31.348Å c: 44.116Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.097 0.097 0.129
Expression system: Not provided

Quick links

Citations

13 review citations

Chemical RNA modifications for studies of RNA structure and dynamics.
Wachowius et al. (2010)
12 more

2 mentions without citation

Mg2+ ions: do they bind to nucleobase nitrogens?
Leonarski et al. (2017)
1 more