1Q8N | pdb_00001q8n

Solution Structure of the Malachite Green RNA Binding Aptamer

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.5mM RNA Aptamer, 10mM phosphate buffer	100% D2O	10mM KCl	5.8	ambient	298
2	2D TOCSY	1.5mM RNA Aptamer, 10mM phosphate buffer	100% D2O	10mM KCl	5.8	ambient	298
3	DQF-COSY	1.5mM RNA Aptamer, 10mM phosphate buffer	100% D2O	10mM KCl	5.8	ambient	298
4	3D_13C-separated_NOESY	1mM RNA Aptamer U-15N,13C, 10mM phosphate buffer	100% D2O	10mM KCl	5.8	ambient	298
5	2D HMQC	1mM RNA Aptamer U-15N,13C, 10mM phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM KCl	5.8	ambient	274
6	HCNCH	1mM RNA Aptamer U-15N,13C, 10mM phosphate buffer	100% D2O	10mM KCl	5.8	ambient	298
7	2D NOESY	1.5mM RNA Aptamer, 10mM phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM KCl	5.8	ambient	274

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

NMR Refinement
Method	Details	Software
simulated annealing	The structure was based on 423 NOE constraints (148 intranucleotide, 119 sequential, 66 medium to long range, and 90 RNA to ligand NOEs) and 219 dihedral angle restraints.	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	25
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	This structure was determined with the aid of the crystal structure of a similar RNA aptamer.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.6	Bruker
2	structure solution	CNS	1.1	A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M.R ice, T. Simonson, G.L. Warren
3	data analysis	XEASY	1.3.13	C. Bartels, T.H. Xia, M. Billeter, P. Gntert and K. Wthrich
4	refinement	CNS	1.1	A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M.R ice, T. Simonson, G.L. Warren