2MBZ | pdb_00002mbz

Structural Basis of a Thiopeptide Antibiotic Multidrug Resistance System from Streptomyces lividans:Promothiocin A in Complex with TipAS

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 mM [U-98% 15N] TipAS-1, 2 mM promothiocin A-2, 50 mM potassium phosphate-3, 0.02 w/v sodium azide-4	95% H2O/5% D2O	0.055	5.9	ambient	298
2	2D 1H-13C HSQC aliphatic	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
3	3D HNCO	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
4	3D CBCA(CO)NH	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
5	3D C(CO)NH TOCSY	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
6	3D HBHA(CO)NH	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
7	3D H(CCO)NH TOCSY	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
8	3D HCCH-TOCSY aliphatic	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
9	3D HNHA	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
10	HAHB	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
11	CBCANH	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
12	13C'-{13C } spin-echo difference 1H-15N HSQC	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
13	15N-{13C } spin-echo difference 1H-15N HSQC	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
14	13C'-{13C } spin-echo difference 1H-13C HSQC	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
15	15N-{13C } spin-echo difference 1H-13C HSQC	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
16	3D 1H-15N ROESY	1 mM [U-98% 15N] TipAS-1, 2 mM promothiocin A-2, 50 mM potassium phosphate-3, 0.02 w/v sodium azide-4	95% H2O/5% D2O	0.055	5.9	ambient	298
17	3D 1H-15N NOESY	1 mM [U-98% 15N] TipAS-1, 2 mM promothiocin A-2, 50 mM potassium phosphate-3, 0.02 w/v sodium azide-4	95% H2O/5% D2O	0.055	5.9	ambient	298
18	3D 1H-13C NOESY	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
19	4D 13C-13C-NOESY-HMQC	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
20	2D NOESY filtered against 1H bound to 13C or 15N	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
21	2D NOESY filtered against 1H bound to 13C or 15N	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
22	2D HOHAHA filtered against 1H bound to 13C or 15N	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298
23	Doublet-separated sensitivity-enhanced 1H-15N HSQC	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
24	Doublet-separated sensitivity-enhanced 1H-15N HSQC	0.8 mM [U-100% 13C; U-100% 15N] TipAS-13, 1.6 mM promothiocin A-14, 10 mM potassium phosphate-15, 10 mg/mL Pf1 phage-16	95% H2O/5% D2O	0.055	5.9	ambient	298
25	J-resolved constant-time 13C-HSQC	1 mM [U-100% 13C; U-100% 15N] TipAS-5, 2 mM promothiocin A-6, 50 mM potassium phosphate-7, 0.02 w/v sodium azide-8	95% H2O/5% D2O	0.055	5.9	ambient	298
26	J-resolved constant-time 13C-HSQC	0.8 mM [U-100% 13C; U-100% 15N] TipAS-13, 1.6 mM promothiocin A-14, 10 mM potassium phosphate-15, 10 mg/mL Pf1 phage-16	95% H2O/5% D2O	0.055	5.9	ambient	298
27	3D 1H-13C NOESY aromatic	1 mM [U-100% 13C; U-100% 15N] TipAS-9, 2 mM promothiocin A-10, 50 mM potassium phosphate-11, 0.02 w/v sodium azide-12	100% D2O	0.055	5.9	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600
2	Bruker	DRX	800

NMR Refinement
Method	Details	Software
simulated annealing	1st. simulated annealing step: ligand is covalently attached, but only restraints of the folded part of the protein in apo form are used 2nd. simulated annealing step: all restraints are used	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR NIH	2.30	Schwieters, Kuszewski, Tjandra and Clore
2	refinement	X-PLOR NIH	2.30	Schwieters, Kuszewski, Tjandra and Clore
3	processing	NMRPipe	2012	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	peak picking	Sparky	3.115	Goddard
5	chemical shift assignment	Sparky	3.115	Goddard
6	peak picking	PIPP		Garrett
7	chemical shift assignment	XEASY		Bartels et al.
8	dihedral angle prediction	TALOS	talos+	Cornilescu, Delaglio and Bax
9	structure analysis	ProcheckNMR		Laskowski and MacArthur
10	experiment/data collection	XwinNMR		Bruker Biospin
11	experiment/data collection	TopSpin		Bruker Biospin