7D8K | pdb_00007d8k

Solution structure of the methyl-CpG binding domain of MBD6 from Arabidopsis thaliana

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	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
2	3D HNCO	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
3	3D HN(CA)CO	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
4	3D CBCA(CO)NH	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
5	3D HNCACB	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
6	2D 1H-13C HSQC aliphatic	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
7	2D 1H-13C HSQC aromatic	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
8	3D CC(CO)NH	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
9	3D H(CC)(CO)NH	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
10	3D HBHA(CO)NH	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
11	3D HBHANH	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
12	3D HCCH-TOCSY	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
13	3D HCCH-COSY	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
14	2D (HB)CB(CGCD)HD	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
15	2D (HB)CB(CGCDCE)HE	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
16	3D 1H-15N NOESY	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
17	3D 1H-13C NOESY aliphatic	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
18	3D 1H-13C NOESY aromatic	1.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE II 700
19	2D IPAP 1H-15N HSQC	0.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE 600
20	2D IPAP 1H-15N HSQC	0.5 mM [U-13C; U-15N] AtMBD6 MBD domain, 20 mM sodium phosphate, 50 mM sodium chloride, 4 % C12E5, 1.2 % 1-hexanol	95% H2O/5% D2O	50 mM	6.5	1 atm	293	Bruker AVANCE 600

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

NMR Refinement
Method	Details	Software
simulated annealing		X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	500
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	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
7	data analysis	TALOS+		Shen, Delaglio, and Cornilescu
3	chemical shift assignment	MagRO-NMRView		Kobayashi (MagRO), Johnson and Blevins (NMRView)
4	data analysis	CcpNmr Analysis		CCPN
5	data analysis	TopSpin		Bruker Biospin
6	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax