BMRBj - BMREntryMaster

Found 1 Document (0.425 seconds)

BMRB: 27436

Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana

Authors

Iwakawa, N., Mahana, Y., Ono, A., Ohki, I., Walinda, E., Morimoto, D., Sugase, K., Shirakawa, M.

Assembly

MBD6

Entity

1. MBD6 (polymer, Thiol state: not present), 68 monomers, 7757.476 Da Detail

GPLGSDNWLP PGWRVEDKIR TSGATAGSVD KYYYEPNTGR KFRSRTEVLY YLEHGTSKRG TKKAENTY

Formula weight

7757.476 Da

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 97.0 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.0 % (769 of 793)	96.2 % (400 of 416)	99.0 % (305 of 308)	92.8 % (64 of 69)
Backbone	98.3 % (393 of 400)	97.9 % (137 of 140)	98.5 % (193 of 196)	98.4 % (63 of 64)
Sidechain	96.2 % (436 of 453)	95.3 % (263 of 276)	100.0 % (172 of 172)	20.0 % (1 of 5)
Aromatic	97.7 % (84 of 86)	97.7 % (42 of 43)	100.0 % (41 of 41)	50.0 % (1 of 2)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. AtMBD6

GPLGSDNWLP PGWRVEDKIR TSGATAGSVD KYYYEPNTGR KFRSRTEVLY YLEHGTSKRG TKKAENTY

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	AtMBD6	[U-100% 13C; U-100% 15N]	5 mM
2	D2O	[U-2H]	5 %
3	H2O	natural abundance	95 %
4	sodium chloride	natural abundance	50 mM
5	sodium phosphate	natural abundance	20 mM

LACS Plot; CA

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

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Release date

2018-03-28

Citation

Backbone and side-chain resonance assignments of the methyl-CpG-binding domain of MBD6 from Arabidopsis thaliana
Iwakawa, N., Mahana, Y., Ono, A., Ohki, I., Walinda, E., Morimoto, D., Sugase, K., Shirakawa, M.
Biomol. NMR Assign. (2018), 13, 59-62, PubMed 30242623 , DOI 10.1007/s12104-018-9851-2 , Abstract

Related entities 1. MBD6, : 2 : 10 entities Detail

Interaction partners 1. MBD6, : 16 interactors Detail

More details for 16 interactors identified by 1 citations

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr27436_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
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)

None

Non-standard residues

None

Content subtype: bmr27436_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	823		98.5 (chain: 1, length: 68)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 68, Sequence coverage: 98.5%
- Total number of assignments
  - ¹H chemical shifts: 454
  - ¹³C chemical shifts: 305
  - ¹⁵N chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
40	ARG	HH11	8.582
40	ARG	HH12	8.582

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	416	400	96.2
¹³C chemical shifts	308	305	99.0
¹⁵N chemical shifts	75	64	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	137	97.9
¹³C chemical shifts	136	133	97.8
¹⁵N chemical shifts	64	63	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	276	263	95.3
¹³C chemical shifts	172	172	100.0
¹⁵N chemical shifts	11	1	9.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	42	97.7
¹³C chemical shifts	41	41	100.0
¹⁵N chemical shifts	2	1	50.0

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Found 1 Document (0.425 seconds)

BMRB: 27436

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MBD6, : 2 : 10 entities Detail

Interaction partners 1. MBD6, : 16 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail