7A05 | pdb_00007a05

NMR structure of D3-D4 domains of Vibrio vulnificus ribosomal protein S1

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.3 mM [U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
2	3D HNHA	1.3 mM [U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
3	3D HNCA	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
4	3D HN(CO)CA	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
5	3D HNCACB	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
6	3D HN(COCA)CB	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 600
7	3D HNCO	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 600
8	3D HN(CA)CO	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 600
9	3D CC(CO)NH	0.7 mM [U-13C; U-15N; 60%-2H] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 700
10	3D HCC(CO)NH	0.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 700
11	3D HCCH-TOCSY	0.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 600
12	3D 1H-15N NOESY	1.3 mM [U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
13	2D 1H-13C HSQC aliphatic	0.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
14	2D 1H-13C HSQC aromatic	0.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
15	3D 1H-13C NOESY aliphatic	0.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
16	3D 1H-13C NOESY aromatic	0.9 mM [U-13C; U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 950
17	2D 1H-15N IPAP-HSQC	1.3 mM [U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 600
18	2D 1H-15N IPAP-HSQC	1.3 mM [U-15N] rS1-D34, 25 mM potassium phosphate, 150 mM potassium chloride, 5 mM DTT	95% H2O/5% D2O	208 mM	7.2	ambient mbar	303	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	700
3	Bruker	AVANCE	800
4	Bruker	AVANCE	900
5	Bruker	AVANCE	950

NMR Refinement
Method	Details	Software
simulated annealing with torsian angle dynamics	structure determination	CYANA
cartesian angle dynamics	energy minimization	CNS
molecular dynamics	refinement in water	ARIA

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	3.x 4.x	Bruker Biospin
2	processing	TopSpin	3.x 4.x	Bruker Biospin
3	chemical shift assignment	Sparky	3.114	Goddard and Kneller
4	peak picking	Sparky	3.114	Goddard and Kneller
5	data analysis	Sparky	3.114	Goddard and Kneller
6	structure calculation	CYANA	3.x	Guntert, Mumenthaler and Wuthrich
7	structure calculation	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
8	refinement	ARIA	1.2 HJ	Linge, O'Donoghue and Nilges
9	data analysis	TALOS-N		Shen and Bax
10	data analysis	PALES		Zweckstetter and Bax