2L5Z | pdb_00002l5z

NMR structure of the A730 loop of the Neurospora VS ribozyme

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-13C CT-HSQC	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
2	2D 1H-13C HMQC	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
3	2D 1H-15N MQ-(HC)N(C)H	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
4	3D CT-HCCH-COSY	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
5	3D HCCH-TOCSY	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
6	3D 13C-edited HMQC-NOESY	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
7	1D flip-back watergate 1H	0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-1	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
8	2D flip-back watergate NOESY	0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-1	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
9	2D imino- and amino-optimized 2D 1H-15N HSQC	0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-3	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
10	2D H(NCCC)H for uracil and cytosine residues	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-5	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
11	2D H(NC)-TOCSY-(C)H for guanosine residues	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-5	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
12	2D (H)N(C)-TOCSY-(C)H for adenosine residues	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-5	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
13	2D 1H-15N CPMG-NOESY	0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-3	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
14	2D 1H 15N HMQC optimized for transfers via J=7.0 Hz and J=21 Hz	0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-4	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
15	2D HNN-COSY	0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-3	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
16	2D DQF-COSY	0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-2	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
17	3D HCCH-E.COSY	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
18	2D imino-optimized 2D 1H-15N HSQC	0.4 mM [U-15N] VS ribozyme SVI RNA (26-MER)-7	90% H2O/10% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
19	Spin-state selective experiments	0.4 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-8	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288
20	Spin-state selective experiments	0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6	100% D2O	50 mM KCl and 5 mM MgCl2	6.5	ambient atm	288

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500
2	Varian	INOVA	600
3	Varian	INOVA	800

NMR Refinement
Method	Details	Software
simulated annealing, molecular dynamics		Module

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	500
Conformers Submitted Total Number	21
Representative Model	1 (minimized average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	Module	1.0	(Module)
2	data analysis	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	data analysis	NMRView		Johnson, One Moon Scientific
4	chemical shift assignment	NMRView		Johnson, One Moon Scientific
5	peak picking	NMRView		Johnson, One Moon Scientific
6	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
7	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
8	structure analysis	Curves+		(CURVES) Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K.
9	structure display	PyMOL		PyMol (Schr dinger)
10	structure analysis	PyMOL		PyMol (Schr dinger)