4OCB
Z-DNA dodecamer d(CGCGCGCGCGCG)2 at 0.75 A resolution solved by P-SAD
Summary for 4OCB
| Entry DOI | 10.2210/pdb4ocb/pdb |
| Related | 3P4J |
| Descriptor | d(CGCGCGCGCGCG)2 duplex (2 entities in total) |
| Functional Keywords | z-dna dodecamer duplex, dna |
| Total number of polymer chains | 1 |
| Total formula weight | 3665.37 |
| Authors | Luo, Z.,Dauter, M.,Dauter, Z. (deposition date: 2014-01-08, release date: 2014-01-22, Last modification date: 2024-02-28) |
| Primary citation | Luo, Z.,Dauter, M.,Dauter, Z. Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution Acta Crystallogr.,Sect.D, D70:1790-1800, 2014 Cited by PubMed Abstract: A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12.2% and an R(free) of 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: Z(I), with the phosphate groups inclined towards the inside of the helix, and Z(II), with the phosphate groups rotated towards the outside of the helix. PubMed: 25004957DOI: 10.1107/S1399004714004684 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (0.75 Å) |
Structure validation
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