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BMRB: 19328

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

Authors

Hassan, F., Ramelot, T.A., Yang, Y., Cort, J.R., Janjua, H., Kohan, E., Lee, D., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Kennedy, M.A.

Assembly

HR7375C

Entity

1. HR7375C (polymer, Thiol state: all other bound), 61 monomers, 6832.663 Da Detail

SHMCPAVSCL QPEGDEVDWV QCDGSCNQWF HQVCVGVSPE MAEKEDYICV RCTVKDAPSR K

2. HR7375C, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

6963.481 Da

Max. entity weight

6832.663 Da

Entity Connection

disulfide 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	2:ZN1:ZN
2	disulfide	sing	1:CYS9:SG	2:ZN1:ZN
3	disulfide	sing	1:CYS34:SG	2:ZN1:ZN
4	disulfide	sing	1:HIS31:NE2	2:ZN1:ZN
5	disulfide	sing	1:CYS49:SG	2:ZN1:ZN
6	disulfide	sing	1:CYS52:SG	2:ZN1:ZN
7	disulfide	sing	1:CYS26:SG	2:ZN1:ZN
8	disulfide	sing	1:CYS22:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, null

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 96.3 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (650 of 675)	96.9 % (340 of 351)	95.4 % (248 of 260)	96.9 % (62 of 64)
Backbone	96.6 % (346 of 358)	97.5 % (118 of 121)	96.1 % (173 of 180)	96.5 % (55 of 57)
Sidechain	96.3 % (361 of 375)	96.5 % (222 of 230)	95.7 % (132 of 138)	100.0 % (7 of 7)
Aromatic	88.0 % (44 of 50)	88.0 % (22 of 25)	87.0 % (20 of 23)	100.0 % (2 of 2)
Methyl	100.0 % (48 of 48)	100.0 % (24 of 24)	100.0 % (24 of 24)

1. HR7375C

SHMCPAVSCL QPEGDEVDWV QCDGSCNQWF HQVCVGVSPE MAEKEDYICV RCTVKDAPSR K

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.006, 90% H2O/10% D2O at PNNL, Richland, WA

#	Name	Isotope labeling	Concentration
10	HR7375C.006	[U-100% 13C; U-100% 15N]	1.04 mM
11	NaN3	natural abundance	0.02 %
12	DTT	natural abundance	10 mM
13	CaCL2	natural abundance	5 mM
14	NaCL	natural abundance	100 mM
15	Proteinase Inhibitors	natural abundance	1 na
16	MES pH 6.5	natural abundance	20 mM
17	D2O	natural abundance	10 %
18	DSS	natural abundance	50 uM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.33 mM HR7375C.007, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
19	HR7375C.007	[U-100% 15N] 5% 13C fractionally labeled	0.33 mM
20	NaN3	natural abundance	0.02 %
21	DTT	natural abundance	10 mM
22	CaCL2	natural abundance	5 mM
23	NaCL	natural abundance	100 mM
24	Proteinase Inhibitors	natural abundance	1 na
25	MES pH 6.5	natural abundance	20 mM
26	D2O	natural abundance	10 %
27	DSS	natural abundance	50 uM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 100% D2O

#	Name	Isotope labeling	Concentration
28	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
29	NaN3	natural abundance	0.02 %
30	DTT	natural abundance	10 mM
31	CaCL2	natural abundance	5 mM
32	NaCL	natural abundance	100 mM
33	Proteinase Inhibitors	natural abundance	1 na
34	MES pH 6.5	natural abundance	20 mM
35	D2O	natural abundance	100 %
36	DSS	natural abundance	50 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.36 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.36 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MA5, Strand ID: A Detail

Release date

2013-08-01

Related entities 1. HR7375C, : 1 : 99 entities Detail

Interaction partners 1. HR7375C, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 26 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

3 3D 1H-15N NOESY NUS

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

4 3D 1H-13C NOESY aliphatic NUS

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

5 3D 1H-13C NOESY aromatic NUS

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

6 2D 1H-15N HSQC

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.33 mM HR7375C.007, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
19	HR7375C.007	[U-100% 15N] 5% 13C fractionally labeled	0.33 mM
20	NaN3	natural abundance	0.02 %
21	DTT	natural abundance	10 mM
22	CaCL2	natural abundance	5 mM
23	NaCL	natural abundance	100 mM
24	Proteinase Inhibitors	natural abundance	1 na
25	MES pH 6.5	natural abundance	20 mM
26	D2O	natural abundance	10 %
27	DSS	natural abundance	50 uM

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.33 mM HR7375C.007, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
19	HR7375C.007	[U-100% 15N] 5% 13C fractionally labeled	0.33 mM
20	NaN3	natural abundance	0.02 %
21	DTT	natural abundance	10 mM
22	CaCL2	natural abundance	5 mM
23	NaCL	natural abundance	100 mM
24	Proteinase Inhibitors	natural abundance	1 na
25	MES pH 6.5	natural abundance	20 mM
26	D2O	natural abundance	10 %
27	DSS	natural abundance	50 uM

8 2D 1H-15N HSQC HIS

Instrument

Bruker Avance II - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.33 mM HR7375C.007, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
19	HR7375C.007	[U-100% 15N] 5% 13C fractionally labeled	0.33 mM
20	NaN3	natural abundance	0.02 %
21	DTT	natural abundance	10 mM
22	CaCL2	natural abundance	5 mM
23	NaCL	natural abundance	100 mM
24	Proteinase Inhibitors	natural abundance	1 na
25	MES pH 6.5	natural abundance	20 mM
26	D2O	natural abundance	10 %
27	DSS	natural abundance	50 uM

9 1D 1H-15N HSQC T1 array

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

10 1D 1H-15N HSQC T2 array

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

11 2D 1H-15N HSQC NH2 only

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

12 2D 1H-13C HSQC aromatic ct

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

13 2D 1H-13C HSQC aromatic noct

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

14 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

15 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

16 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

17 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

18 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

19 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

20 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

21 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

22 3D CCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM

23 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.005, 100% D2O

#	Name	Isotope labeling	Concentration
28	HR7375C.005	[U-100% 13C; U-100% 15N]	1.04 mM
29	NaN3	natural abundance	0.02 %
30	DTT	natural abundance	10 mM
31	CaCL2	natural abundance	5 mM
32	NaCL	natural abundance	100 mM
33	Proteinase Inhibitors	natural abundance	1 na
34	MES pH 6.5	natural abundance	20 mM
35	D2O	natural abundance	100 %
36	DSS	natural abundance	50 uM

24 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.006, 90% H2O/10% D2O at PNNL, Richland, WA

#	Name	Isotope labeling	Concentration
10	HR7375C.006	[U-100% 13C; U-100% 15N]	1.04 mM
11	NaN3	natural abundance	0.02 %
12	DTT	natural abundance	10 mM
13	CaCL2	natural abundance	5 mM
14	NaCL	natural abundance	100 mM
15	Proteinase Inhibitors	natural abundance	1 na
16	MES pH 6.5	natural abundance	20 mM
17	D2O	natural abundance	10 %
18	DSS	natural abundance	50 uM

25 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.006, 90% H2O/10% D2O at PNNL, Richland, WA

#	Name	Isotope labeling	Concentration
10	HR7375C.006	[U-100% 13C; U-100% 15N]	1.04 mM
11	NaN3	natural abundance	0.02 %
12	DTT	natural abundance	10 mM
13	CaCL2	natural abundance	5 mM
14	NaCL	natural abundance	100 mM
15	Proteinase Inhibitors	natural abundance	1 na
16	MES pH 6.5	natural abundance	20 mM
17	D2O	natural abundance	10 %
18	DSS	natural abundance	50 uM

26 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM HR7375C.006, 90% H2O/10% D2O at PNNL, Richland, WA

#	Name	Isotope labeling	Concentration
10	HR7375C.006	[U-100% 13C; U-100% 15N]	1.04 mM
11	NaN3	natural abundance	0.02 %
12	DTT	natural abundance	10 mM
13	CaCL2	natural abundance	5 mM
14	NaCL	natural abundance	100 mM
15	Proteinase Inhibitors	natural abundance	1 na
16	MES pH 6.5	natural abundance	20 mM
17	D2O	natural abundance	10 %
18	DSS	natural abundance	50 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19328_2ma5.nef
Input source #2: Coordindates	2ma5.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:31:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:49:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:4:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:52:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:26:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:22:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:9:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:34:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60-
SHMCPAVSCLQPEGDEVDWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVKDAPSRK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SHMCPAVSCLQPEGDEVDWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVKDAPSRK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0

Content subtype: combined_19328_2ma5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	653		98.4 (chain: A, length: 61)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	705 (1)	noe	98.4 (chain: A, length: 61)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	22 (1)	hbond	32.8 (chain: A, length: 61)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	46 (46)	.	54.1 (chain: A, length: 61)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 340
  - ¹³C chemical shifts: 251
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
21	GLN	CD	179.8
27	ASN	CG	177.7
28	GLN	CD	180.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	351	340	96.9
¹³C chemical shifts	260	248	95.4
¹⁵N chemical shifts	66	62	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	118	97.5
¹³C chemical shifts	122	116	95.1
¹⁵N chemical shifts	57	55	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	230	222	96.5
¹³C chemical shifts	138	132	95.7
¹⁵N chemical shifts	9	7	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	25	96.2
¹³C chemical shifts	26	24	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	22	88.0
¹³C chemical shifts	23	20	87.0
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
- Total number of restraints: 705
- Weight of restraints: 1.0 (705)
- Potential type of restraints: square-well-parabolic (705)
- Range of distance target values: 2.3, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 32.8%
  - Total number of restraints: 22
  - Weight of restraints: 1.0 (22)
  - Potential type of restraints: square-well-parabolic (22)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 54.1%
- Total number of restraints: 46
- Total number of restraints per polymer type: 46
- Weight of restraints: 1.0 (46)
- Potential type of restraints: square-well-parabolic (46)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Structural Genomics, Protein NMR, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Target HR7375C, PSI-Biology, Protein Structure Initiative, Zinc binding protein, PHD

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Found 1 Document (0.81 seconds)

BMRB: 19328

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR7375C, : 1 : 99 entities Detail

Interaction partners 1. HR7375C, : 4 interactors Detail

Experiments performed 26 experiments Detail

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