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1o15
From Proteopedia
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| - | [[Image:1o15.gif|left|200px]]<br /><applet load="1o15" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1o15" /> | ||
| - | '''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 /> | ||
| - | == | + | ==THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS== |
| + | <StructureSection load='1o15' size='340' side='right'caption='[[1o15]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | ||
| + | <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> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
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 </=2 A and an R-factor </=25%; the latter is based on 131 RNA crystal structures solved at a resolution of </=3 A and an R-factor of </=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 </=2 A and an R-factor </=25%; the latter is based on 131 RNA crystal structures solved at a resolution of </=3 A and an R-factor of </=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. | ||
| - | + | 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> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 1o15" style="background-color:#fffaf0;"></div> |
| - | [[Category: Clore | + | == References == |
| - | [[Category: Kuszewski | + | <references/> |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Clore GM]] | |
| + | [[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
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