1K5I

NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5	90% H2O/10% D2O	10 mM Sodium Phosphate	6.5	ambient	298
2	DQF-COSY	0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5	90% H2O/10% D2O	10 mM Sodium Phosphate	6.5	ambient	298
3	1H-31P HETCOR	0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5	90% H2O/10% D2O	10 mM Sodium Phosphate	6.5	ambient	298
4	COSY-35	0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5	90% H2O/10% D2O	10 mM Sodium Phosphate	6.5	ambient	298
5	TOCSY	0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5	90% H2O/10% D2O	10 mM Sodium Phosphate	6.5	ambient	298
6		0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5	90% H2O/10% D2O	10 mM Sodium Phosphate	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AMX	600

NMR Refinement
Method	Details	Software
Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics	A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form distances) distance restraints for the stem region and 143 dihedral angle restraints. Additionally, 50 distance restraints were used to maintain the Watson-Crick geometry of the base pairs in the stem region. Final refinement resulted in 10 lowest energy structures.	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	33
Conformers Submitted Total Number	10

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.1	Brunger

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.