BMRBj - BMREntryMaster

Found 1 Document (0.749 seconds)

BMRB: 16936

2KY8

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

Authors

Williams, D.C., Scarsdale, J.N.

Assembly

MBD2 bound to a methylated DNA

Entity

1. cMBD2 (polymer, Thiol state: all free), 72 monomers, 7991.085 Da Detail

GSDKQGRTDC PALPPGWKKE EVIRKSGLSA GKSDVYYFSP SGKKFRSKPQ LARYLGNAVD LSCFDFRTGK MM

2. DNA-strand 1 (polymer, Thiol state: not present), 11 monomers, 3639.440 Da Detail

GGAATXGGCX C

3. DNA-strand 2 (polymer, Thiol state: not present), 11 monomers, 3599.416 Da Detail

GAGCXGATXC C

4. MN (non-polymer), 54.938 × 2 Da

Total weight

15339.817 Da

Max. entity weight

7991.085 Da

Source organism

Gallus gallus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.3 %, Completeness: 84.5 %, Completeness (bb): 78.8 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	84.5 % (862 of 1020)	78.3 % (488 of 623)	94.2 % (307 of 326)	94.4 % (67 of 71)
Backbone	78.8 % (432 of 548)	64.1 % (175 of 273)	93.3 % (194 of 208)	94.0 % (63 of 67)
Sidechain	91.8 % (492 of 536)	89.4 % (313 of 350)	96.2 % (175 of 182)	100.0 % (4 of 4)
Aromatic	77.7 % (87 of 112)	73.0 % (54 of 74)	86.5 % (32 of 37)	100.0 % (1 of 1)
Methyl	98.0 % (49 of 50)	96.2 % (25 of 26)	100.0 % (24 of 24)

1. cMBD2

GSDKQGRTDC PALPPGWKKE EVIRKSGLSA GKSDVYYFSP SGKKFRSKPQ LARYLGNAVD LSCFDFRTGK MM

2. DNA-strand 1

GGAATXGGCX C

3. DNA-strand 2

GAGCXGATXC C

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
8	cMBD2	[U-13C; U-15N; U-2H]	0.8 mM
9	DNA-strand_1	natural abundance	0.8 mM
10	DNA-strand_2	natural abundance	0.8 mM
11	pf1 bacteriophage	natural abundance	12 mg/mL
12	phosphate	natural abundance	10 mM
13	sodium azide	natural abundance	0.02 %
14	D20	natural abundance	10 %
15	H20	natural abundance	90 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, 10% D2O

#	Name	Isotope labeling	Concentration
16	cMBD2	[U-13C; U-15N; U-2H]	0.5 mM
17	DNA-strand_1	natural abundance	0.5 mM
18	DNA-strand_2	natural abundance	0.5 mM
19	MANGANESE (II) ION	natural abundance	0.5 mM
20	phosphate	natural abundance	10 mM
21	sodium azide	natural abundance	0.02 %
22	D20	natural abundance	10 %
23	H20	natural abundance	90 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, 10% D2O

#	Name	Isotope labeling	Concentration
24	cMBD2	[U-13C; U-15N; U-2H]	0.5 mM
25	DNA-strand_1	natural abundance	0.5 mM
26	DNA-strand_2	natural abundance	0.5 mM
27	CA2+	natural abundance	0.5 mM
28	phosphate	natural abundance	10 mM
29	sodium azide	natural abundance	0.02 %
30	D20	natural abundance	10 %
31	H20	natural abundance	90 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2KY8, Strand ID: A Detail

Release date

2011-06-20

Citation

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence
Scarsdale, J., Webb, H.D., Ginder, G.D., Williams, D.C.
Nucleic Acids Res. (2011), 39, 6741-6752, PubMed 21531701 , DOI 10.1093/nar/gkr262 , Abstract

Related entities 1. cMBD2, : 1 : 15 : 61 entities Detail

Experiments performed 23 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

2 3D HNCO

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

3 3D HNCA

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

4 3D HN(CO)CA

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

5 3D HNCACB

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

6 3D CBCA(CO)NH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

7 3D HCCH-TOCSY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

8 3D C(CO)NH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

9 3D C(CO)NH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

10 3D CCH-TOCSY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

11 3D 1H-15N NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

13 3D 1H-13C NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

14 2D 13C,15N filtered NOESY

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

15 2D 1H-15N HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
8	cMBD2	[U-13C; U-15N; U-2H]	0.8 mM
9	DNA-strand_1	natural abundance	0.8 mM
10	DNA-strand_2	natural abundance	0.8 mM
11	pf1 bacteriophage	natural abundance	12 mg/mL
12	phosphate	natural abundance	10 mM
13	sodium azide	natural abundance	0.02 %
14	D20	natural abundance	10 %
15	H20	natural abundance	90 %

16 2D 1H-15N HSQC-T1

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, 10% D2O

#	Name	Isotope labeling	Concentration
16	cMBD2	[U-13C; U-15N; U-2H]	0.5 mM
17	DNA-strand_1	natural abundance	0.5 mM
18	DNA-strand_2	natural abundance	0.5 mM
19	MANGANESE (II) ION	natural abundance	0.5 mM
20	phosphate	natural abundance	10 mM
21	sodium azide	natural abundance	0.02 %
22	D20	natural abundance	10 %
23	H20	natural abundance	90 %

17 2D 1H-15N HSQC-T1

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, 10% D2O

#	Name	Isotope labeling	Concentration
24	cMBD2	[U-13C; U-15N; U-2H]	0.5 mM
25	DNA-strand_1	natural abundance	0.5 mM
26	DNA-strand_2	natural abundance	0.5 mM
27	CA2+	natural abundance	0.5 mM
28	phosphate	natural abundance	10 mM
29	sodium azide	natural abundance	0.02 %
30	D20	natural abundance	10 %
31	H20	natural abundance	90 %

18 3D-HNCO-JNH

Instrument

Varian UnityPlus - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
8	cMBD2	[U-13C; U-15N; U-2H]	0.8 mM
9	DNA-strand_1	natural abundance	0.8 mM
10	DNA-strand_2	natural abundance	0.8 mM
11	pf1 bacteriophage	natural abundance	12 mg/mL
12	phosphate	natural abundance	10 mM
13	sodium azide	natural abundance	0.02 %
14	D20	natural abundance	10 %
15	H20	natural abundance	90 %

19 3D-HNCO-JNH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

20 2D 1H-15N HSQC,JNCO

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

21 2D 1H-15N HSQC.JNCO

Instrument

Varian UnityPlus - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
8	cMBD2	[U-13C; U-15N; U-2H]	0.8 mM
9	DNA-strand_1	natural abundance	0.8 mM
10	DNA-strand_2	natural abundance	0.8 mM
11	pf1 bacteriophage	natural abundance	12 mg/mL
12	phosphate	natural abundance	10 mM
13	sodium azide	natural abundance	0.02 %
14	D20	natural abundance	10 %
15	H20	natural abundance	90 %

22 3D HNCO,JCOCA

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
1	cMBD2	[U-99% 13C; U-99% 15N]	1 mM
2	DNA-strand_1	natural abundance	1 mM
3	DNA-strand_2	natural abundance	1 mM
4	phosphate	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	D20	natural abundance	10 %
7	H20	natural abundance	90 %

23 3D HNCO,JCOCA

Instrument

Varian UnityPlus - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10mM PO4, 0.02% sodium azide, pH 6.5

#	Name	Isotope labeling	Concentration
8	cMBD2	[U-13C; U-15N; U-2H]	0.8 mM
9	DNA-strand_1	natural abundance	0.8 mM
10	DNA-strand_2	natural abundance	0.8 mM
11	pf1 bacteriophage	natural abundance	12 mg/mL
12	phosphate	natural abundance	10 mM
13	sodium azide	natural abundance	0.02 %
14	D20	natural abundance	10 %
15	H20	natural abundance	90 %

nullKeywords DNA methylation, MBD2, paramagnetic relaxation enhancement, structural dynamics

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Found 1 Document (0.749 seconds)

BMRB: 16936

Sample #1

Sample #2

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Related entities 1. cMBD2, : 1 : 15 : 61 entities Detail

Experiments performed 23 experiments Detail

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