5JZQ

Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations

Summary for 5JZQ

• Entry DOI: 10.2210/pdb5jzq/pdb
• Related: 1ICK 1VTU 3P4J 4HIF 4HIG 4R15 5EBI
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: z-dna duplex, self-complementary duplex, centrosymmetric space group, dna enantiomer; racemate, l-ribose nucleic acid; disorder; macromolecular phase problem, ab initio methods, dual-space methods, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 3693.32

Authors

Drozdzal, P.,Gilski, M.,Jaskolski, M. (deposition date: 2016-05-17, release date: 2016-11-09, Last modification date: 2024-05-08)

Primary citation

Drozdzal, P.,Gilski, M.,Jaskolski, M.
Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.
Acta Crystallogr D Struct Biol, 72:1203-1211, 2016

PubMed Abstract: The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2'-deoxyribose (the natural enantiomer) and L-2'-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 Å resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg sites. The crystal structure is comprised of both left-handed (D-form) and right-handed (L-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented D/L-DNA-Mg structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG) duplex with those of other homochiral and heterochiral Z-DNA structures.

PubMed: 27841753
DOI: 10.1107/S205979831601679X

Experimental method

X-RAY DIFFRACTION (0.78 Å)