6V88 | pdb_00006v88

Solution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D [15N, 1H]-HSQC	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
2	2D [13C, 1H] CT-HSQC aliphatic	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
3	2D [13C, 1H] CT-HSQC aromatic	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
4	3D 13C/15N-edited [1H,1H] NOESY	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
5	3D TROSY-HNCACB	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
6	3D (H)CCH-COSY aromatic	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
7	3D (H)CCH-COSY aliphatic	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
8	3D (H)CCH-TOCSY aliphatic	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Bruker AVANCE NEO 800
9	3D 13C/15N-filtered 13C/15N-edited [1H,1H] NOESY	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Agilent VNMRS 600
14	3D CBCA(CO)NH	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Agilent VNMRS 600
13	3D HBHA(CO)NH	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Agilent VNMRS 600
12	3D HNCO	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Agilent VNMRS 600
15	3D (HCA)CONH	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Agilent VNMRS 600
11	2D long-range [15N, 1H]-HSQC	0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide	90% H2O/10% D2O	50 mM	6.0	1 atm	308	Agilent VNMRS 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE NEO	800
2	Agilent	VNMRS	600

NMR Refinement
Method	Details	Software
simulated annealing	Refinement in explicit water bath	CNS

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
8	processing	TopSpin		Bruker Biospin
9	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
10	data analysis	CARA		Keller and Wuthrich
11	chemical shift assignment	CARA		Keller and Wuthrich
12	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
13	peak picking	CARA		Keller and Wuthrich
14	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
15	collection	TopSpin		Bruker Biospin
16	collection	VNMR		Varian
17	data analysis	TALOS		Cornilescu, Delaglio and Bax
18	data analysis	PSVS		Bhattacharya and Montelione