100d: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:100d.gif|left|200px]]<br />
-<applet load="100d" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="100d, resolution 1.900&Aring;" />
-'''CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING==
-The crystal structure of the self-complementary chimeric decamer duplex, r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved, at 1.9 A resolution by the molecular replacement method and refined to an, R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the, terminal riboses apparently drive the entire chimeric duplex into an A-DNA, conformation, in contrast to the B-DNA conformation adopted by the, all-deoxy decamer of the same sequence. Five symmetry related duplexes, encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and, hydrogen bonding interactions. The spermine interaction severely bends the, duplexes by 31 degrees into the major groove at the fourth base ... [[http://ispc.weizmann.ac.il/pmbin/getpm?7816639 (full description)]]
+<StructureSection load='100d' size='340' side='right'caption='[[100d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[100d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=100D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=100D FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene></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=100d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=100d OCA], [https://pdbe.org/100d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=100d RCSB], [https://www.ebi.ac.uk/pdbsum/100d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=100d ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the self-complementary chimeric decamer duplex r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved at 1.9 A resolution by the molecular replacement method and refined to an R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the terminal riboses apparently drive the entire chimeric duplex into an A-DNA conformation, in contrast to the B-DNA conformation adopted by the all-deoxy decamer of the same sequence. Five symmetry related duplexes encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and hydrogen bonding interactions. The spermine interaction severely bends the duplexes by 31 degrees into the major groove at the fourth base pair G(4).C(17), jolts it and slides the 'base plate' into the minor groove. This base pair, together with the adjacent base pair in the top half and the corresponding pseudo two-fold related base pairs in the bottom half, form four minor groove base-paired multiples with the terminal base pairs of two neighboring duplexes.
-==About this Structure==
+Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing.,Ban C, Ramakrishnan B, Sundaralingam M Nucleic Acids Res. 1994 Dec 11;22(24):5466-76. PMID:7816639<ref>PMID:7816639</ref>
-D is a [[http://en.wikipedia.org/wiki/Protein_complex Protein complex]] structure of sequences from [[http://en.wikipedia.org/wiki/ ]] with SPM as [[http://en.wikipedia.org/wiki/ligand ligand]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id= OCA]].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing., Ban C, Ramakrishnan B, Sundaralingam M, Nucleic Acids Res. 1994 Dec 11;22(24):5466-76. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7816639 7816639]
+</div>
-[[Category: Protein complex]]
+<div class="pdbe-citations 100d" style="background-color:#fffaf0;"></div>
-[[Category: Ban, C.]]
+== References ==
-[[Category: Ramakrishnan, B.]]
+<references/>
-[[Category: Sundaralingam, M.]]
+__TOC__
-[[Category: SPM]]
+</StructureSection>
-[[Category: a-dna/rna]]
+[[Category: Large Structures]]
-[[Category: double helix]]
+[[Category: Ban C]]
+[[Category: Ramakrishnan B]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 15:37:40 2007''
+[[Category: Sundaralingam M]]