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 1.3 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
  • Primary Citation of Related Structures:  
    1O15

  • 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 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 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: 
    • 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 Biol 4: 644
    • 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

    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 nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
THEOPHYLLINE-BINDING RNAA33N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEP
Query on TEP

Download Ideal Coordinates CCD File 
B [auth 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



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Advisory, Data collection, Database references, Derived calculations