1D93

STRUCTURAL VARIATION IN D(CTCTAGAG). IMPLICATIONS FOR PROTEIN-DNA INTERACTIONS

Summary for 1D93

• Entry DOI: 10.2210/pdb1d93/pdb
• Descriptor: DNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 1
• Total formula weight: 2426.62

Authors

Hunter, W.N.,Langlois D'Estaintot, B.,Kennard, O. (deposition date: 1992-10-17, release date: 1993-07-15, Last modification date: 2024-02-07)

Primary citation

Hunter, W.N.,D'Estaintot, B.L.,Kennard, O.
Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions.
Biochemistry, 28:2444-2451, 1989

PubMed Abstract: Single-crystal X-ray diffraction techniques have been used to characterize the structure of the self-complementary DNA oligomer d(CTCTAGAG). The structure was refined to an R factor of 14.7% using data to 2.15-A resolution. The tetragonal unit cell, space group P4(3)2(1)2, has dimensions a = 42.53 and c = 24.33 A. The asymmetric unit consists of a single strand or four base pairs. Two strands, related by a crystallographic dyad axis, coil about each other to form a right-handed duplex. This octamer duplex has a mean helix rotation of 32 degrees, 11.3 base pairs per turn, an average rise of 3.1 A, C3'-endo furanose conformations, a shallow minor groove, and a deep major groove. Such averaged parameters suggest classification of the octamer as a member of the A-DNA family. However, the global parameters tend to mask variations in conformational parameters observed at the level of the base pairs. In particular, the central TpA (= TpA) step displays extensive interstrand purine-purine overlap and an unusual sugar-phosphate backbone conformation. These structural features may be directly related to certain sequence-specific protein-DNA interactions involving nucleases and repressors.

PubMed: 2730875
DOI: 10.1021/bi00432a015

Experimental method

X-RAY DIFFRACTION (2.15 Å)