5dnb: Difference between revisions

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-{{Seed}}
-[[Image:5dnb.png|left|200px]]
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+==STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-G==
-The line below this paragraph, containing "STRUCTURE_5dnb", creates the "Structure Box" on the page.
+<StructureSection load='5dnb' size='340' side='right'caption='[[5dnb]], [[Resolution|resolution]] 1.40&Aring;' 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'>[[5dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DNB 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]] 1.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_5dnb|  PDB=5dnb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnb OCA], [https://pdbe.org/5dnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dnb RCSB], [https://www.ebi.ac.uk/pdbsum/5dnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnb ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the DNA decamer C-C-A-A-C-G-T-T-G-G has been solved to a resolution of 1.4 A, and is compared with the 1.3 A structure of C-C-A-A-G-A-T-T-G-G and the 1.6 A structure of C-C-A-G-G-C-C-T-G-G. All three decamers crystallize isomorphously in space group C2 with five base-pairs per asymmetric unit, and with decamer double helices stacked atop one another along the c axis in a manner that closely approximates a continuous B helix. This efficient stacking probably accounts for the high resolution of the crystal data. Comparison of the three decamers reveals the following. (1) Minor groove width is more variable than heretofore realized. Regions of A.T base-pairs tend to be narrower than average, although two successive A.T base-pairs alone may not be sufficient to produce narrowing. The minor groove is wider in regions where BII phosphate conformations are opposed diagonally across the groove. (2) Narrow regions of minor groove exhibit a zig-zag spine of hydration, as was first seen in C-G-C-G-A-A-T-T-C-G-C-G, whereas wide regions show two ribbons of water molecules down the walls, connecting base edge N or O with sugar O-4' atoms. Regions of intermediate groove width may accommodate neither pattern of hydration well, and may exhibit a less regular pattern of hydration. (3) Base-pair stacking is virtually identical at equivalent positions in the three decamers. The unconnected step from the top of one decamer helix to the bottom of the next helix is a normal helix step in all respects, except for the absence of connecting phosphate groups. (4) BII phosphate conformation require the unstacking of the two bases linked by the phosphate, but do not necessarily follow as an inevitable consequence of unstacking. They have an influence on minor groove width as noted in point (1) above. (5) Sugar ring pseudorotation P and main-chain torsion angle delta show an excellent correlation as given by the equation: delta = 40 degrees cos (P + 144 degrees) + 120 degrees. Although centered around C-2'-endo, the conformations in these B-DNA helices are distributed broadly from C-3'-exo to O-4'-endo, unlike the tighter clustering around C-3'-endo observed in A-DNA oligomer structures.
-===STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-G===
+Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G.,Prive GG, Yanagi K, Dickerson RE J Mol Biol. 1991 Jan 5;217(1):177-99. PMID:1988677<ref>PMID:1988677</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_1988677}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 5dnb" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 1988677 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_1988677}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DNB OCA].
+[[Category: Dickerson RE]]
+[[Category: Prive GG]]
-==Reference==
+[[Category: Yanagi K]]
-Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G., Prive GG, Yanagi K, Dickerson RE, J Mol Biol. 1991 Jan 5;217(1):177-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1988677 1988677]
-[[Category: Dickerson, R E.]]
-[[Category: Prive, G G.]]
-[[Category: Yanagi, K.]]
-[[Category: B-dna]]
-[[Category: Double helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul  3 14:00:33 2008''