2MA5

Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	3D 1H-15N NOESY NUS	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	3D 1H-13C NOESY aliphatic NUS	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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-13C NOESY aromatic NUS	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	2D 1H-15N HSQC	0.33 mM [U-100% 15N] 5% 13C fractionally labeled HR7375C.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
7	2D 1H-13C HSQC aliphatic	0.33 mM [U-100% 15N] 5% 13C fractionally labeled HR7375C.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
8	2D 1H-15N HSQC HIS	0.33 mM [U-100% 15N] 5% 13C fractionally labeled HR7375C.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
9	1D 1H-15N HSQC T1 array	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	1D 1H-15N HSQC T2 array	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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
11	2D 1H-15N HSQC NH2 only	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	2D 1H-13C HSQC aromatic ct	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	2D 1H-13C HSQC aromatic noct	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	3D HNCACB	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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
15	3D CBCA(CO)NH	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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
16	3D HN(CO)CA	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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
17	3D HNCO	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	3D HBHA(CO)NH	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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 C(CO)NH	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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 H(CCO)NH	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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 HCCH-TOCSY	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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 CCH-TOCSY	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.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
24	3D 1H-15N NOESY	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.006, 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
25	3D 1H-13C NOESY aliphatic	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.006, 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
26	3D 1H-13C NOESY aromatic	1.04 mM [U-100% 13C; U-100% 15N] HR7375C.006, 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	Varian	INOVA	750

NMR Refinement
Method	Details	Software
simulated annealing, null	CNS water refinement of Cyana structures, 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//nmrbin.linux9	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	collection	TopSpin	2.4	Bruker Biospin
6	collection	VnmrJ		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	fmcgui2.1_linux	Alex Lemak, Cheryl Arrowmith
12	refinement	CNS

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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2MA5

Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C