2KY8 | pdb_00002ky8

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
2	3D HNCO	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
3	3D HNCA	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
4	3D HN(CO)CA	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
5	3D HNCACB	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
6	3D CBCA(CO)NH	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
7	3D HCCH-TOCSY	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
8	3D C(CO)NH	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
9	3D C(CO)NH	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
10	3D CCH-TOCSY	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
11	3D 1H-15N NOESY	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
12	3D 1H-15N NOESY	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
13	3D 1H-13C NOESY	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
14	2D 13C,15N filtered NOESY	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
15	2D 1H-15N HSQC	0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage	90% H2O/10% D2O	20	6.5	ambient	298
16	2D 1H-15N HSQC-T1	0.5 mM [U-13C; U-15N; U-2H] cMBD2, 0.5 mM DNA, 0.5 mM MANGANESE (II) ION	90% H2O/10% D2O	20	6.5	ambient	298
17	2D 1H-15N HSQC-T1	0.5 mM [U-13C; U-15N; U-2H] cMBD2, 0.5 mM DNA, 0.5 mM CA2+	90% H2O/10% D2O	20	6.5	ambient	298
18	3D-HNCO-JNH	0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage	90% H2O/10% D2O	20	6.5	ambient	298
19	3D-HNCO-JNH	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
20	2D 1H-15N HSQC,JNCO	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
21	2D 1H-15N HSQC.JNCO	0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage	90% H2O/10% D2O	20	6.5	ambient	298
22	3D HNCO,JCOCA	1 mM [U-99% 13C; U-99% 15N] cMBD2, 1 mM DNA	90% H2O/10% D2O	20	6.5	ambient	298
23	3D HNCO,JCOCA	0.8 mM [U-13C; U-15N; U-2H] cMBD2, 0.8 mM DNA, 12 mg/mL of1 bacteriophage	90% H2O/10% D2O	20	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	UNITYPLUS	500
2	Bruker	AVANCE	700

NMR Refinement
Method	Details	Software
torsion angle dynamics	experimental target function included NOE distances, backbone torsion angle restraints based on chemical shifts, residual dipolar couplings and paramagnetic relaxation enhancement data.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	20
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
2	chemical shift assignment	PIPP		Garrett
3	peak picking	PIPP		Garrett
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	collection	TopSpin		Bruker Biospin
6	collection	VNMR		Varian