167d: Difference between revisions

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<StructureSection load='167d' size='340' side='right'caption='[[167d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='167d' size='340' side='right'caption='[[167d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=167D FirstGlance]. <br>
<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>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=167d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=167d OCA], [http://pdbe.org/167d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=167d RCSB], [http://www.ebi.ac.uk/pdbsum/167d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=167d ProSAT]</span></td></tr>
</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>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:8196049<ref>PMID:8196049</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 167d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Dickerson, R E]]
[[Category: Dickerson RE]]
[[Category: Goodsell, D S]]
[[Category: Goodsell DS]]
[[Category: Kaczor-Grzeskowiak, M]]
[[Category: Kaczor-Grzeskowiak M]]
[[Category: B-dna]]
[[Category: Dna]]
[[Category: Double helix]]

Latest revision as of 09:25, 7 February 2024

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

Structural highlights

167d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

167d, resolution 2.30Å

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