3P4J

Ultra-high resolution structure of d(CGCGCG)2 Z-DNA

Summary for 3P4J

• Entry DOI: 10.2210/pdb3p4j/pdb
• Related: 1D48 1DCG 1I0T 1ICK 2DCG
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), SPERMINE (3 entities in total)
• Functional Keywords: z-dna, dna
• Total number of polymer chains: 2
• Total formula weight: 3822.75

Authors

Brzezinski, K.,Brzuszkiewicz, A.,Dauter, M.,Kubicki, M.,Jaskolski, M.,Dauter, Z. (deposition date: 2010-10-06, release date: 2011-08-24, Last modification date: 2023-09-06)

Primary citation

Brzezinski, K.,Brzuszkiewicz, A.,Dauter, M.,Kubicki, M.,Jaskolski, M.,Dauter, Z.
High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.
Nucleic Acids Res., 39:6238-6248, 2011

PubMed Abstract: The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

PubMed: 21459852
DOI: 10.1093/nar/gkr202

Experimental method

X-RAY DIFFRACTION (0.55 Å)