7EN4 | pdb_00007en4

Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HNCA	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
2	3D HN(CO)CA	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
3	3D CBCA(CO)NH	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
4	3D CBCANH	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
5	3D HBHA(CO)NH	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
11	3D H(CCO)NH	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
10	3D C(CO)NH	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
9	3D HCCH-TOCSY	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
8	3D 1H-13C NOESY	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
7	3D 1H-15N NOESY	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
6	3D HSQC-NOESY-HSQC	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
12	3D H(CCO)NH	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
14	3D CCNH	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
13	3D C(CO)NH	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
16	2D 1H-1H TOCSY	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
15	3D 1H-13C NOESY	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
17	3D 1H-15N NOESY	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
18	3D TROSY-HNCO	2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE 600
21	T1 relaxation	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 600
20	T2 relaxation	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 600
19	heteronuclear 1H-15N NOE	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 600
23	T1 relaxation	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 700
22	T2 relaxation	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 700
24	heteronuclear 1H-15N NOE	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 700
25	2D 1H-15N HSQC	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 600
27	2D 1H-13C HSQC	2 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 600
26	2D 1H-15N IPAP HSQC	2 mM [U-100% 15N] ubiquitin hydrolase	90% H2O/10% D2O	100 mM	6.0	AMBIENT Pa	303	Bruker AVANCE III 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE III	600
3	Bruker	AVANCE III	700

NMR Refinement
Method	Details	Software
energy minimization		OPAL

NMR Ensemble Information
Conformer Selection Criteria	structures randomly selected from each of five clusters
Conformers Calculated Total Number	20
Conformers Submitted Total Number	20
Representative Model	1 (closest the center of the largest cluster)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure calculation	CYANA	3.99.0	Guntert, Mumenthaler and Wuthrich
2	processing	Azara	2.8.1	Boucher
3	chemical shift assignment	CcpNmr Analysis	2.5.0	CCPN
4	collection	TopSpin	3.5	Bruker Biospin
5	refinement	OPAL	1.4	Luginbuhl, Guntert, Billeter and Wuthrich
6	peak picking	CcpNmr Analysis	2.5.0	CCPN