1o15: Difference between revisions

Revision as of 03:13, 3 May 2008

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

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 Sat May 3 03:13:46 2008

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OCA

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 [[Image:1o15.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1o15 |SIZE=350|CAPTION= <scene name='initialview01'>1o15</scene>
+The line below this paragraph, containing "STRUCTURE_1o15", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=TEP:THEOPHYLLINE'>TEP</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1o15|  PDB=1o15  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o15 OCA], [http://www.ebi.ac.uk/pdbsum/1o15 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1o15 RCSB]</span>
-}}
 '''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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 ==About this Structure==
-O15 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].
+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: ribonucleic acid]]
+[[Category: Ribonucleic acid]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 03:13:46 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:38:16 2008''