Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.82 kDa 
• Atom Count: 717 
• Modelled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique nucleic acid chains: 1

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

• PDB DOI: 10.2210/pdb1O15/pdb
• NDB: 1O15

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-10-21 Released: 2003-02-18 
• Deposition Author(s): Clore, G.M., Kuszewski, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 250 
• Conformers Submitted: 1 
• Selection Criteria: RESTRAINED REGULARIZED MEAN STRUCTURE 

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

• PubMed: 12568611 
• 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 former is based on 416 nucleic acid crystal structures solved at a resolution of

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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

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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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
THEOPHYLLINE-BINDING RNA	A	33	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TEP	B [auth A]	THEOPHYLLINE C7 H8 N4 O2 ZFXYFBGIUFBOJW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 250 
• Conformers Submitted: 1 
• Selection Criteria: RESTRAINED REGULARIZED MEAN STRUCTURE 
• OLDERADO: 1O15 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-21 
• Released Date: 2003-02-18 
Deposition Author(s): Clore, G.M., Kuszewski, J.

Revision History  

• 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