116d
From Proteopedia
(New page: 200px<br /><applet load="116d" size="450" color="white" frame="true" align="right" spinBox="true" caption="116d, resolution 2.500Å" /> '''CRYSTAL AND MOLECUL...) |
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| - | [[Image:116d.gif|left|200px]]<br /><applet load="116d" size=" | + | [[Image:116d.gif|left|200px]]<br /><applet load="116d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="116d, resolution 2.500Å" /> | caption="116d, resolution 2.500Å" /> | ||
'''CRYSTAL AND MOLECULAR STRUCTURE OF THE A-DNA DODECAMER D(CCGTACGTACGG): CHOICE OF FRAGMENT HELICAL AXIS'''<br /> | '''CRYSTAL AND MOLECULAR STRUCTURE OF THE A-DNA DODECAMER D(CCGTACGTACGG): CHOICE OF FRAGMENT HELICAL AXIS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the dodecamer d(CCGTACGTACGG) has been determined | + | The crystal structure of the dodecamer d(CCGTACGTACGG) has been determined at 2.5 A resolution. The crystals grow in the hexagonal space group P6(1)22, a = b = 46.2 A, c = 71.5 A with one strand as the asymmetric unit. Diffraction data were collected by the oscillation film method yielding 1664 unique reflections with an Rmerge of 0.04. The structure was solved by real-space rotational translational searches with idealized helical models of A, B and Z-DNA. The best agreement was given by an A-DNA model with its dyad axis along the diagonal crystallographic dyad axis, with an R-factor 0.43 and correlation coefficient of 0.59 for data between 10 and 5 A. Iterative map fitting and restrained least-squares refinement and addition of 40 solvent molecules brought the R-factor to 0.15 and the correlation coefficient to 0.97 for all data between 8.0 and 2.5 A. The stereochemistry of the atomic model is good, with a root-mean-square deviation in bond distances of 0.006 A. This is the first example of an A-DNA containing a full helical turn. The dodecamer displays a novel packing motif. In addition to the characteristic contacts between the terminal base-pairs and the minor grooves of symmetry-related molecules, there are also minor groove to minor groove interactions not previously observed. The packing leaves an approximately 25 A diameter solvent channel around the origin, along the c-axis. The presence of a prominent 3.4 A meridional reflection and other diffuse features in the diffraction pattern provided evidence for the presence of disordered B-DNA along the c-axis, which can be accommodated in these solvent channels. The molecular conformation of the dodecamer also displays novel features. The dyad-related halves of the molecule are bent at an angle of 20 degrees, and the helical parameters are affected by this bend. Unlike the shorter A-DNA octamers, the dimensions of the major groove can be directly measured. Novel correlations between local helical parameters and global conformational features are presented. Most of the solvent molecules are associated with the major groove and the sugar-phosphate backbone. |
==About this Structure== | ==About this Structure== | ||
| - | 116D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 116D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=116D OCA]. |
==Reference== | ==Reference== | ||
Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis., Bingman CA, Zon G, Sundaralingam M, J Mol Biol. 1992 Oct 5;227(3):738-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1404387 1404387] | Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis., Bingman CA, Zon G, Sundaralingam M, J Mol Biol. 1992 Oct 5;227(3):738-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1404387 1404387] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Bingman, C | + | [[Category: Bingman, C A.]] |
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
[[Category: Zon, G.]] | [[Category: Zon, G.]] | ||
| Line 18: | Line 18: | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:37:40 2008'' |
Revision as of 09:37, 21 February 2008
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CRYSTAL AND MOLECULAR STRUCTURE OF THE A-DNA DODECAMER D(CCGTACGTACGG): CHOICE OF FRAGMENT HELICAL AXIS
Overview
The crystal structure of the dodecamer d(CCGTACGTACGG) has been determined at 2.5 A resolution. The crystals grow in the hexagonal space group P6(1)22, a = b = 46.2 A, c = 71.5 A with one strand as the asymmetric unit. Diffraction data were collected by the oscillation film method yielding 1664 unique reflections with an Rmerge of 0.04. The structure was solved by real-space rotational translational searches with idealized helical models of A, B and Z-DNA. The best agreement was given by an A-DNA model with its dyad axis along the diagonal crystallographic dyad axis, with an R-factor 0.43 and correlation coefficient of 0.59 for data between 10 and 5 A. Iterative map fitting and restrained least-squares refinement and addition of 40 solvent molecules brought the R-factor to 0.15 and the correlation coefficient to 0.97 for all data between 8.0 and 2.5 A. The stereochemistry of the atomic model is good, with a root-mean-square deviation in bond distances of 0.006 A. This is the first example of an A-DNA containing a full helical turn. The dodecamer displays a novel packing motif. In addition to the characteristic contacts between the terminal base-pairs and the minor grooves of symmetry-related molecules, there are also minor groove to minor groove interactions not previously observed. The packing leaves an approximately 25 A diameter solvent channel around the origin, along the c-axis. The presence of a prominent 3.4 A meridional reflection and other diffuse features in the diffraction pattern provided evidence for the presence of disordered B-DNA along the c-axis, which can be accommodated in these solvent channels. The molecular conformation of the dodecamer also displays novel features. The dyad-related halves of the molecule are bent at an angle of 20 degrees, and the helical parameters are affected by this bend. Unlike the shorter A-DNA octamers, the dimensions of the major groove can be directly measured. Novel correlations between local helical parameters and global conformational features are presented. Most of the solvent molecules are associated with the major groove and the sugar-phosphate backbone.
About this Structure
116D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis., Bingman CA, Zon G, Sundaralingam M, J Mol Biol. 1992 Oct 5;227(3):738-56. PMID:1404387
Page seeded by OCA on Thu Feb 21 11:37:40 2008
