1o15

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(New page: 200px<br /><applet load="1o15" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o15" /> '''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THE...)
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[[Image:1o15.gif|left|200px]]<br /><applet load="1o15" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1o15" />
 
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'''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS'''<br />
 
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==Overview==
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==THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS==
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The description of the nonbonded contact terms used in simulated annealing, refinement can have a major impact on nucleic acid structures generated, from NMR data. Using complete dipolar coupling cross-validation, we, demonstrate that substantial improvements in coordinate accuracy of NMR, structures of RNA can be obtained by making use of two conformational, database potentials of mean force: a nucleic acid torsion angle database, potential consisting of various multidimensional torsion angle, correlations; and an RNA specific base-base positioning potential that, provides a simple geometric, statistically based, description of, sequential and nonsequential base-base interactions. The former is based, on 416 nucleic acid crystal structures solved at a resolution of &lt;/=2 A, and an R-factor &lt;/=25%; the latter is based on 131 RNA crystal structures, solved at a resolution of &lt;/=3 A and an R-factor of &lt;/=25%, and includes, both the large and small subunits of the ribosome. The application of, these two database potentials is illustrated for the structure refinement, of an RNA aptamer/theophylline complex for which extensive NOE and, residual dipolar coupling data have been measured in solution.
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<StructureSection load='1o15' size='340' side='right'caption='[[1o15]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1o15]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O15 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TEP:THEOPHYLLINE'>TEP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o15 OCA], [https://pdbe.org/1o15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o15 RCSB], [https://www.ebi.ac.uk/pdbsum/1o15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o15 ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The description of the nonbonded contact terms used in simulated annealing refinement can have a major impact on nucleic acid structures generated from NMR data. Using complete dipolar coupling cross-validation, we demonstrate that substantial improvements in coordinate accuracy of NMR structures of RNA can be obtained by making use of two conformational database potentials of mean force: a nucleic acid torsion angle database potential consisting of various multidimensional torsion angle correlations; and an RNA specific base-base positioning potential that provides a simple geometric, statistically based, description of sequential and nonsequential base-base interactions. The former is based on 416 nucleic acid crystal structures solved at a resolution of &lt;/=2 A and an R-factor &lt;/=25%; the latter is based on 131 RNA crystal structures solved at a resolution of &lt;/=3 A and an R-factor of &lt;/=25%, and includes both the large and small subunits of the ribosome. The application of these two database potentials is illustrated for the structure refinement of an RNA aptamer/theophylline complex for which extensive NOE and residual dipolar coupling data have been measured in solution.
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==About this Structure==
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Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation.,Clore GM, Kuszewski J J Am Chem Soc. 2003 Feb 12;125(6):1518-25. PMID:12568611<ref>PMID:12568611</ref>
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1O15 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with TEP as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1O15 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation., Clore GM, Kuszewski J, J Am Chem Soc. 2003 Feb 12;125(6):1518-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12568611 12568611]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1o15" style="background-color:#fffaf0;"></div>
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[[Category: Clore, G.M.]]
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== References ==
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[[Category: Kuszewski, J.]]
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<references/>
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[[Category: TEP]]
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__TOC__
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[[Category: ribonucleic acid]]
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</StructureSection>
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[[Category: Large Structures]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:11:23 2007''
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[[Category: Clore GM]]
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[[Category: Kuszewski J]]

Current revision

THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS

PDB ID 1o15

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