1o15: Difference between revisions
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[[Image:1o15.gif|left|200px]] | [[Image:1o15.gif|left|200px]] | ||
'''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS''' | {{Structure | ||
|PDB= 1o15 |SIZE=350|CAPTION= <scene name='initialview01'>1o15</scene> | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=TEP:THEOPHYLLINE'>TEP</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1O15 is a [ | 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== | ==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:// | 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: Protein complex]] | ||
[[Category: Clore, G M.]] | [[Category: Clore, G M.]] | ||
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[[Category: ribonucleic acid]] | [[Category: ribonucleic acid]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:04:18 2008'' | ||
Revision as of 14:04, 20 March 2008
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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
OverviewOverview
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.
About this StructureAbout this Structure
1O15 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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
Page seeded by OCA on Thu Mar 20 13:04:18 2008