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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 250 
  • Conformers Submitted: 
  • Selection Criteria: RESTRAINED REGULARIZED MEAN STRUCTURE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, G.M.Kuszewski, J.

(2003) J.Am.Chem.Soc. 125: 1518-1525

  • DOI: 10.1021/ja028383j

  • PubMed Abstract: 
  • 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 improv ...

    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


    Related Citations: 
    • Refinement of Local and Long Range Structural Order in Theophylline-Binding RNA Using Using 13C-1H Residual Dipolar Couplings and Restrained Molecular Dynamics.
      Sibille, N.,Pardi, A.,Simorre, J.P.,Blackledge, M.
      (2001) J.Am.Chem.Soc. 123: 12135
    • Improving the Accuracy of NMR Structures of DNA by Means of a Database Potential of Mean Force Describing Base-Base Positional Interactions.
      Kuszewski, J.,Schwieters, C.,Clore, G.M.
      (2001) J.Am.Chem.Soc. 123: 3903
    • Interlocking Structural Motifs Mediate Molecular Discrimination by a Theophylline-Binding RNA
      Zimmermann, G.R.,Jenison, R.D.,Wick, C.L.,Simorre, J.P.,Pardi, A.
      (1997) Nat.Struct.Mol.Biol. 4: 644


    Organizational Affiliation

    Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
THEOPHYLLINE-BINDING RNAA33N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEP
Query on TEP

Download SDF File 
Download CCD File 
A
THEOPHYLLINE
C7 H8 N4 O2
ZFXYFBGIUFBOJW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 250 
  • Conformers Submitted: 
  • Selection Criteria: RESTRAINED REGULARIZED MEAN STRUCTURE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance