5EBI

Crystal structure of a DNA-RNA chimera in complex with Ba2+ ions: a case of unusual multi-domain twinning

Summary for 5EBI

• Entry DOI: 10.2210/pdb5ebi/pdb
• Related: 3P4J
• Descriptor: DNA/RNA (5'-D(*C)-R(P*G)-D(P*C)-R(P*G)-D(P*C)-R(P*G)-3'), BARIUM ION (3 entities in total)
• Functional Keywords: dna-rna chimera complex; z-dna; z-rna; self-complementary duplex; left-handed z-type duplex; multi-domain twinning; detection; twin pseudosymmetry, dna-rna chimera complex, dna/rna chimera
• Biological source: synthetic construct
• Total number of polymer chains: 8
• Total formula weight: 17062.87

Authors

Gilski, M.,Drozdzal, P.,Kierzek, R.,Jaskolski, M. (deposition date: 2015-10-19, release date: 2016-02-10, Last modification date: 2024-01-10)

Primary citation

Gilski, M.,Drozdzal, P.,Kierzek, R.,Jaskolski, M.
Atomic resolution structure of a chimeric DNA-RNA Z-type duplex in complex with Ba(2+) ions: a case of complicated multi-domain twinning.
Acta Crystallogr D Struct Biol, 72:211-223, 2016

PubMed Abstract: The self-complementary dCrGdCrGdCrG hexanucleotide, in which not only the pyrimidine/purine bases but also the ribo/deoxy sugars alternate along the sequence, was crystallized in the presence of barium cations in the form of a left-handed Z-type duplex. The asymmetric unit of the P21 crystal with a pseudohexagonal lattice contains four chimeric duplexes and 16 partial Ba(2+) sites. The chimeric (DNA-RNA)2 duplexes have novel patterns of hydration and exhibit a high degree of discrete conformational disorder of their sugar-phosphate backbones, which can at least partly be correlated with the fractional occupancies of the barium ions. The crystals of the DNA-RNA chimeric duplex in complex with Ba(2+) ions and also with Sr(2+) ions exhibit complicated twinning, which in combination with structural pseudosymmetry made structure determination difficult. The structure could be successfully solved by molecular replacement in space groups P1 and P21 but not in orthorhombic or higher symmetry and, after scrupulous twinning and packing analysis, was refined in space group P21 to an R and Rfree of 11.36 and 16.91%, respectively, using data extending to 1.09 Å resolution. With the crystal structure having monoclinic symmetry, the sixfold crystal twinning is a combination of threefold and twofold rotations. The paper describes the practical aspects of dealing with cases of complicated twinning and pseudosymmetry, and compares the available software tools for the refinement and analysis of such cases.

PubMed: 26894669
DOI: 10.1107/S2059798315024365

Experimental method

X-RAY DIFFRACTION (1.09 Å)