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167d

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THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS

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Retrieved from "http://52.214.119.220/wiki/index.php/167d"

Categories: Large Structures | Dickerson RE | Goodsell DS | Kaczor-Grzeskowiak M

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-[[Image:167d.gif|left|200px]]<br /><applet load="167d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="167d, resolution 2.300&Aring;" />
-'''THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS'''<br />
-==Overview==
+==THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS==
-The single-crystal X-ray analysis of trigonal C-C-A-T-T-A-A-T-G-G, and its comparison with orthorhombic C-G-A-T-T-A-A-T-C-G, have shown that the A-T-T-A-A-T sequence has limited polymorphism under the influence of packing forces from neighboring molecules in the crystal. The T-A step is intrinsically variable. It is not inconsistent with a large propeller twist, a narrow minor groove, and a single spine of hydration, as has sometimes been claimed on theoretical grounds. The T-A step does show a persistent positive roll, in a direction that compresses the major groove, and this may be a significant factor in macroscopic DNA curvature induced by phased A-tracts. A-tracts, as understood in this paper, include A-A and A-T steps, but not the T-A step, which is disruptive. Three conclusions regarding A-tract-induced curvature can be drawn from this and other X-ray crystal structure analyses, and from key gel retardation experiments: (1) The A-tract bending model is disqualified on two grounds: (i) tilt-wedge bending within A-tracts is incompatible with the observed direction of curvature; (ii) roll-wedge bending within A-tracts is contradicted by every crystal structure analysis, and is inconsistent with gel retardation results for (G-C-A-A-A-A-T-T-T-T)n and for (A-A-A-A-A-T-T-T-T-T)n. (2) The junction bend model is contradicted by crystallography because: (i) the inclination of base-pairs does not change between A-tract and non-A-tract regions of helix; and (ii) the observed bends at GC/AT junctions are roll-wedge bends, not tilt-wedge as the junction bend model demands. (3) The non-A-tract bending model is consistent with both gel retardation data and with X-ray crystallography, and must be regarded as the only consistent model for A-tract bending.
+<StructureSection load='167d' size='340' side='right'caption='[[167d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[167d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=167D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=167D FirstGlance]. <br>
-D 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=167D OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=167d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=167d OCA], [https://pdbe.org/167d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=167d RCSB], [https://www.ebi.ac.uk/pdbsum/167d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=167d ProSAT]</span></td></tr>
-==Reference==
+</table>
-The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps., Goodsell DS, Kaczor-Grzeskowiak M, Dickerson RE, J Mol Biol. 1994 May 27;239(1):79-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8196049 8196049]
+__TOC__
-[[Category: Protein complex]]
+</StructureSection>
-[[Category: Dickerson, R E.]]
+[[Category: Large Structures]]
-[[Category: Goodsell, D S.]]
+[[Category: Dickerson RE]]
-[[Category: Kaczor-Grzeskowiak, M.]]
+[[Category: Goodsell DS]]
-[[Category: b-dna]]
+[[Category: Kaczor-Grzeskowiak M]]
-[[Category: double helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:38:38 2008''

167d

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THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS

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