9DNA

CRYSTAL STRUCTURE ANALYSIS OF AN A-DNA FRAGMENT AT 1.8 ANGSTROMS RESOLUTION. D(GCCCGGGC)

Summary for 9DNA

• Entry DOI: 10.2210/pdb9dna/pdb
• Descriptor: DNA (5'-D(*GP*CP*CP*CP*GP*GP*GP*C)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 1
• Total formula weight: 2428.59

Authors

Heinemann, U. (deposition date: 1987-07-10, release date: 1988-01-16, Last modification date: 2024-02-14)

Primary citation

Heinemann, U.,Lauble, H.,Frank, R.,Blocker, H.
Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC).
Nucleic Acids Res., 15:9531-9550, 1987

PubMed Abstract: Single crystals of the self-complementary octadeoxyribonucleotide d(GCCCGGGC) have been analysed by X-ray diffraction methods at a resolution of 1.8 A. The tetragonal unit cell of space group P4(3)2(1)2 has dimensions of a = 43.25 A and c = 24.61 A and contains eight strands of the oligonucleotide. The structure was refined by standard crystallographic techniques to an R factor of 17.1% using 1359 3 sigma structure factor observations. Two strands of the oligonucleotide are related by the crystallographic dyad axis to form a DNA helix in the A conformation. The d(GCCCGGGC) helix is characterized by a wide open major groove, a near perpendicular orientation of base pairs to the helix axis and an unusually small average helix twist angle of 31.3 degrees indicating a slightly underwound helix with 11.5 base pairs per turn. Extensive cross-strand stacking between guanine bases at the central cytosine-guanine step is made possible by a number of local conformational adjustments including a fully extended sugar-phosphate backbone of the central guanosine nucleotide.

PubMed: 3684603
DOI: 10.1093/nar/15.22.9531

Experimental method

X-RAY DIFFRACTION (1.8 Å)