2JPP | pdb_00002jpp

Structural basis of RsmA/CsrA RNA recognition: Structure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM [U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
2	3D 1H-15N NOESY	1 mM [U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
3	3D CBCA(CO)NH	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
4	3D HNCA	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
5	3D HNCACB	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
6	3D HNCO	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
7	2D 1H-1H TOCSY	1 mM [U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
8	3D H(CCO)NH	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
9	2D 1H-1H NOESY	1 mM [U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
10	2D 1H-13C HSQC	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	100% D2O	0.18	7.2	ambient	313
11	3D 1H-13C NOESY	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
12	3D HN(CO)CA	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
13	2D 1H-13C HSQC	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA	100% D2O	0.18	7.2	ambient	313
14	3D 1H-13C NOESY	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA	100% D2O	0.18	7.2	ambient	313
15	2D 1H-13C HSQC	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA	100% D2O	0.18	7.2	ambient	313
16	3D 1H-13C NOESY	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA	100% D2O	0.18	7.2	ambient	313
17	2D 1H-15N HSQC	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
18	2D 1H-15N HSQC	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA	93% H2O/7% D2O	0.18	7.2	ambient	313
19	2D 1Ff2Ff NOESY	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	100% D2O	0.18	7.2	ambient	313
20	2D 1Ff2Ff NOESY	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA	100% D2O	0.18	7.2	ambient	313
21	2D 1Ff2Ff NOESY	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA	100% D2O	0.18	7.2	ambient	313
22	3D 1Fe3Ff NOESY	1 mM [U-100% 13C; U-100% 15N] RsmE, 1 mM RNA	100% D2O	0.18	7.2	ambient	313
23	3D 1Fe3Ff NOESY	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Cyt/Ade RNA	100% D2O	0.18	7.2	ambient	313
24	3D 1Fe3Ff NOESY	1 mM [U-100% 15N] RsmE, 1 mM [U-13C; U-15N]-Gua/Ura RNA	100% D2O	0.18	7.2	ambient	313

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DMX	500
2	Bruker	DMX	600
3	Bruker	DMX	750
4	Bruker	AVANCE	900

NMR Refinement
Method	Details	Software
simulated annealing	in implicit water	Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	7.0	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Koll
2	geometry optimization	DYANA	3.02	Guntert, Braun and Wuthrich
3	chemical shift assignment	Sparky		Goddard
4	data analysis	Sparky		Goddard
5	rename chains	CCP4		CCP4 Executuve Committee
6	superpose ensemble	CCP4		CCP4 Executuve Committee

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 R01GM157729.

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Structural basis of RsmA/CsrA RNA recognition: Structure of RsmE bound to the Shine-Dalgarno sequence of hcnA mRNA

2JPP | pdb_00002jpp