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[[Image:1o15.gif|left|200px]]


{{Structure
==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= 1o15 |SIZE=350|CAPTION= <scene name='initialview01'>1o15</scene>
<StructureSection load='1o15' size='340' side='right'caption='[[1o15]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=TEP:THEOPHYLLINE'>TEP</scene>
<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>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
|GENE=  
<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>
}}
<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>
 
</table>
'''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS'''
<div style="background-color:#fffaf0;">
 
== Publication Abstract from PubMed ==
 
==Overview==
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.
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.


==About this Structure==
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>
1O15 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O15 OCA].
 
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/12568611 12568611]
[[Category: Protein complex]]
[[Category: Clore, G M.]]
[[Category: Kuszewski, J.]]
[[Category: TEP]]
[[Category: ribonucleic acid]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:04:18 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1o15" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Clore GM]]
[[Category: Kuszewski J]]

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