PDBsum entry 123d

DNA

PDB id: 123d

Contents

DNA/RNA

Waters ×80

PDB id:

123d

Name:

DNA

Title:

DNA helix structure and refinement algorithm: comparison of models for d(ccaggcm==5==ctgg) derived from nuclsq, tnt, and x-plor

Structure:

DNA (5'-d( Cp Cp Ap Gp Gp Cp (5Cm)p Tp Gp G)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dodecamer (from PQS)

Resolution:

1.70Å R-factor: 0.191

Authors:

M.Hahn,U.Heinemann

Key ref:

M.Hahn and U.Heinemann (1993). DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR. Acta Crystallogr D Biol Crystallogr, 49, 468-477. PubMed id: 15299506 DOI: 10.1107/S0907444993004858

Date:

03-May-93 Release date: 15-Oct-93

DNA/RNA chains

C-C-A-G-G-C-5CM-T-G-G 10 bases

C-C-A-G-G-C-5CM-T-G-G 10 bases

DOI no: 10.1107/S0907444993004858

Acta Crystallogr D Biol Crystallogr 49:468-477 (1993)

PubMed id: 15299506

DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.

M.Hahn, U.Heinemann.

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.

Selected figure(s)

Figure 1.
Fig. 1. Portions of the 2Fo-Fc difference electron-density maps around base pair A(3).T(18) of d(CCAGGCmSCTGG). The maps are contoured at 1.5 times their r.m.s, density. Models and maps are derived from (a) NUCLSQ, (b) TNT and (c) X-PLOR.

Figure 5.
Fig. 5. Average temperature factors (A 2) for the atoms in bases (B), sugars (S) and phosphate groups (P) of d(CCAGGCmSCTGG) after refinement with NUCLSQ (yellow), TNT (red) and X-PLOR (blue).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 468-477) copyright 1993.

Figures were selected by an automated process.