1bdn
From Proteopedia
(New page: 200px<br /> <applet load="1bdn" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bdn, resolution 2.600Å" /> '''CRYSTAL LATTICE PA...) |
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| - | [[Image:1bdn.gif|left|200px]]<br /> | + | [[Image:1bdn.gif|left|200px]]<br /><applet load="1bdn" size="350" color="white" frame="true" align="right" spinBox="true" |
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caption="1bdn, resolution 2.600Å" /> | caption="1bdn, resolution 2.600Å" /> | ||
'''CRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT'''<br /> | '''CRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of a DNA duplex dodecamer d(CGCAAAAATGCG) and its | + | The crystal structure of a DNA duplex dodecamer d(CGCAAAAATGCG) and its complementary strand has been determined at 2.6-A resolution. Although our goal was to deduce the structural features of the static bending of the helical axis exhibited by adenine-tract structures in solution, we conclude that the overall bend of 20 degrees in the direction of the major groove observed here arises from the forces associated with crystal packing. An isomorphous dodecamer brominated on one strand provides experimental evidence that this asymmetric sequence is positioned in two orientations in the crystal lattice that are related by a 180 degrees rotation around the pseudodyad axis of the sequence. The bend in these two differently positioned DNA molecules depends on their orientation in the crystal, not on their sequence. As with previously determined structures containing adenine tracts, the adenine and thymine base pairs are highly propeller twisted. The N-6 of the adenine comes within hydrogen bonding distance of the O-4 of thymine one step down the helix, facilitating the formation of a series of bifurcated hydrogen bonds within the adenine tract. The adenine tract is relatively straight and the bending is localized outside this region. |
==About this Structure== | ==About this Structure== | ||
| - | 1BDN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1BDN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BDN OCA]. |
==Reference== | ==Reference== | ||
Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract., DiGabriele AD, Sanderson MR, Steitz TA, Proc Natl Acad Sci U S A. 1989 Mar;86(6):1816-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2928304 2928304] | Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract., DiGabriele AD, Sanderson MR, Steitz TA, Proc Natl Acad Sci U S A. 1989 Mar;86(6):1816-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2928304 2928304] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: DiGabriele, A | + | [[Category: DiGabriele, A D.]] |
| - | [[Category: Sanderson, M | + | [[Category: Sanderson, M R.]] |
| - | [[Category: Steitz, T | + | [[Category: Steitz, T A.]] |
[[Category: MG]] | [[Category: MG]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:54:14 2008'' |
Revision as of 09:54, 21 February 2008
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CRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT
Overview
The crystal structure of a DNA duplex dodecamer d(CGCAAAAATGCG) and its complementary strand has been determined at 2.6-A resolution. Although our goal was to deduce the structural features of the static bending of the helical axis exhibited by adenine-tract structures in solution, we conclude that the overall bend of 20 degrees in the direction of the major groove observed here arises from the forces associated with crystal packing. An isomorphous dodecamer brominated on one strand provides experimental evidence that this asymmetric sequence is positioned in two orientations in the crystal lattice that are related by a 180 degrees rotation around the pseudodyad axis of the sequence. The bend in these two differently positioned DNA molecules depends on their orientation in the crystal, not on their sequence. As with previously determined structures containing adenine tracts, the adenine and thymine base pairs are highly propeller twisted. The N-6 of the adenine comes within hydrogen bonding distance of the O-4 of thymine one step down the helix, facilitating the formation of a series of bifurcated hydrogen bonds within the adenine tract. The adenine tract is relatively straight and the bending is localized outside this region.
About this Structure
1BDN is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract., DiGabriele AD, Sanderson MR, Steitz TA, Proc Natl Acad Sci U S A. 1989 Mar;86(6):1816-20. PMID:2928304
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