2MA6 | pdb_00002ma6

Solution NMR Structure of the RING finger domain from the Kip1 ubiquitination-promoting E3 complex protein 1 (KPC1/RNF123) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8700A

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
2	2D 1H-13C HSQC aliphatic	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
3	2D 1H-13C HSQC aromatic CT	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
4	2D 1H-13C HSQC aromatic noCT	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
5	3D 1H-15N NOESY	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
6	3D 1H-15N NOESY NUS	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
7	3D 1H-13C NOESY aliphatic	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
8	3D 1H-13C NOESY aliphatic NUS	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
9	3D 1H-13C NOESY aromatic	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
10	2D 1H-13C HSQC aliphatic	1.0 mM [U-100% 13C; U-100% 15N] HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
11	3D C(CO)NH	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
12	3D H(CCO)NH	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
13	3D HCCH-COSY	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
14	2D 1H-15N HSQC	0.9 mM [U-100% 15N] 5% 13C-fractional labeling HR8700A.007, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
15	2D 1H-13C HSQC aliphatic	0.9 mM [U-100% 15N] 5% 13C-fractional labeling HR8700A.007, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
16	2D 1H-15N HSQC HIS	0.9 mM [U-100% 15N] 5% 13C-fractional labeling HR8700A.007, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
17	1D T1 NSQC array	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
18	1D T2 NHSQC array	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
19	3D CBCA(CO)NH	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
20	3D HNCACB	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
21	3D HBHA(CO)NH	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
22	3D HNCO	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
23	2D 1H-15N HSQC NH2 only	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
24	4D HCCH NOESY	1.0 mM [U-100% 13C; U-100% 15N] HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
25	3D CCH-TOCSY	1.0 mM [U-100% 13C; U-100% 15N] HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
26	2D 1H-15N HSQC	1.0 mM [U-100% 13C; U-100% 15N] HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
27	2D 1H-15N HSQC	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298
28	3D HCCH-TOCSY	1.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS	90% H2O/10% D2O		6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE II	850
2	Varian	INOVA	600
3	Bruker	AVANCE III	600

NMR Refinement
Method	Details	Software
simulated annealing, null	CNS water refinement of Cyana structures via fmcGui, null	CNS

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinemen,structure solution,geometry optimization	CNS	1.3	Brunger, Adams, Clore, Gros, Nilges and Read
2	refinement,geometry optimization,structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
3	data analysis,refinement	AutoStructure	2.1	Huang, Tejero, Powers and Montelione
4	processing	NMRPipe	NMRPipe-2008	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	collection	TopSpin	2.4	Bruker Biospin
6	collection	VnmrJ	vnmrj_1.1_D	Varian
7	chemical shift assignment	PINE		Bahrami, Markley, Assadi, and Eghbalnia
8	data analysis	Sparky	3.113	Goddard
9	geometry optimization	TALOS+	Version 1.2009.0721.18	Shen, Cornilescu, Delaglio and Bax
10	structure validation	PSVS	1.4	Bhattacharya, Montelione
11	refinement	FMCGUI	fmcgui2.5_linux	Alex Lemak, Cheryl Arrowmith
12	refinement	CNS