6TPH | pdb_00006tph

Structure of a protein-RNA complex by ssNMR

SOLID-STATE NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NCA	4 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
2	2D NCO	4 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
3	2D 13C,13C DARR	4 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
4	3D NCACX	8 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 5 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
5	3D NCOCX	8 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 5 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
7	3D CANCO	8 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 5 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
6	2D 13C,13C DARR	8 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 5 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
8	2D 13C,13C SPC53	8 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 5 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	265	Bruker AVANCE III 600
9	2D 13C,13C SPC53	4 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 12 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 10 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
10	2D 13C,13C SPC53	16 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ade RNA (26-MER), 8 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
12	2D 13C,13C SPC53	16 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ura RNA (26-MER), 8 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
11	2D 13C,13C SPC53	4 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 12 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 10 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
13	2D 13C,13C SPC53	16 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ade RNA (26-MER), 8 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
14	2D 13C,13C SPC53	16 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ura RNA (26-MER), 8 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
15	2D 13C,13C SPC53	4 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 12 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 10 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
16	2D 13C,13C SPC53	16 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ade RNA (26-MER), 8 mg/mL RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600
17	2D 13C,13C SPC53	16 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ura RNA (26-MER), 8 mg/L RNA (26-MER)	solid	150 mM	7.6	1 bar	260	Bruker AVANCE III 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	600

NMR Refinement
Method	Details	Software
na	10 structures with best haddock score were subjected to 15 ns of MD simulation.	Amber

NMR Ensemble Information
Conformer Selection Criteria	target function
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		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	structure calculation	HADDOCK		Bonvin
3	chemical shift assignment	CARA		Keller and Wuthrich
4	peak picking	CARA		Keller and Wuthrich
5	collection	TopSpin		Bruker Biospin