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| [[Image:1vj4.gif|left|200px]]
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| <!--
| | ==SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)== |
| The line below this paragraph, containing "STRUCTURE_1vj4", creates the "Structure Box" on the page.
| | <StructureSection load='1vj4' size='340' side='right'caption='[[1vj4]], [[Resolution|resolution]] 1.80Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[1vj4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJ4 FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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=1vj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vj4 OCA], [https://pdbe.org/1vj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1vj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vj4 ProSAT]</span></td></tr> |
| {{STRUCTURE_1vj4| PDB=1vj4 | SCENE= }}
| | </table> |
| | | __TOC__ |
| '''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)'''
| | </StructureSection> |
| | | [[Category: Large Structures]] |
| | | [[Category: Cruse WB]] |
| ==Overview== | | [[Category: Kennard O]] |
| The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.
| | [[Category: Rabinovich D]] |
| | | [[Category: Salisbury SA]] |
| ==About this Structure==
| | [[Category: Shakked Z]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJ4 OCA]. | | [[Category: Viswamitra MA]] |
| | |
| ==Reference== | |
| Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6854642 6854642]
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| [[Category: Cruse, W B.]] | |
| [[Category: Kennard, O.]] | |
| [[Category: Rabinovich, D.]] | |
| [[Category: Salisbury, S A.]] | |
| [[Category: Shakked, Z.]] | |
| [[Category: Viswamitra, M A.]] | |
| [[Category: A-dna]] | |
| [[Category: Double helix]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:35:14 2008''
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