123D

DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR

Summary for 123D

• Entry DOI: 10.2210/pdb123d/pdb
• Descriptor: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(5CM)P*TP*GP*G)-3') (2 entities in total)
• Functional Keywords: b-dna, double helix, modified, dna
• Total number of polymer chains: 2
• Total formula weight: 6120.04

Authors

Hahn, M.,Heinemann, U. (deposition date: 1993-05-03, release date: 1993-10-15, Last modification date: 2024-02-07)

Primary citation

Hahn, M.,Heinemann, U.
DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.
Acta Crystallogr.,Sect.D, 49:468-477, 1993

PubMed Abstract: In an earlier study [Heinemann & Hahn (1992). J. Biol. Chem. 267, 7332-7341], the crystal structure of the double-stranded B-DNA decamer d(CCAGGCm(5)CTGG) was refined with NUCLSQ to R = 17.4% against 3799 2sigma structure amplitudes in the resolution range 8-1.7 A. This structure has now been re-refined against the same diffraction data using either TNT or X-PLOR in order to determine to what extent the resulting DNA conformations would differ and to examine the suitability of these programs for the refinement of oligonucleotide structures. The R value from the NUCLSQ refinement could not be reached with either TNT or X-PLOR, although both programs yield reasonably refined DNA models showing root-mean-square deviations against the NUCLSQ model of the decamer duplex of 0.25 and 0.32 A, respectively. Some derived local structure parameters differ depending on the refinement procedure used. This holds true for several exocyclic torsion angles of the sugar-phosphate backbone, whereas sugar puckers as well as helical and base-pair stacking parameters are only weakly influenced. A subset of 15 solvent sites with low temperature factors is conserved in all three models.

PubMed: 15299506
DOI: 10.1107/S0907444993004858

Experimental method

X-RAY DIFFRACTION (1.7 Å)