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BMRB: 18963

2M3H

1H, 13C, 15N chemical shift assignments of Dido PHD domain

Authors

Santiveri, C.M., Perez-Canadillas, J.M., Jimenez, M.

Assembly

Dido PHD

Entity

1. Dido PHD (polymer, Thiol state: all free), 61 monomers, 7039.975 Da Detail

GSMDPNALYC ICRQPHNNRF MICCDRCEEW FHGDCVGISE ARGRLLERNG EDYICPNCTI L

2. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

7170.793 Da

Max. entity weight

7039.975 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 96.7 %, Completeness: 59.9 %, Completeness (bb): 46.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.9 % (413 of 690)	95.3 % (345 of 362)	21.7 % (57 of 263)	16.9 % (11 of 65)
Backbone	46.7 % (168 of 360)	95.2 % (118 of 124)	21.9 % (39 of 178)	19.0 % (11 of 58)
Sidechain	66.6 % (257 of 386)	95.4 % (227 of 238)	21.3 % (30 of 141)	0.0 % (0 of 7)
Aromatic	46.4 % (26 of 56)	92.9 % (26 of 28)	0.0 % (0 of 27)	0.0 % (0 of 1)
Methyl	63.0 % (29 of 46)	91.3 % (21 of 23)	34.8 % (8 of 23)

1. Dido PHD

GSMDPNALYC ICRQPHNNRF MICCDRCEEW FHGDCVGISE ARGRLLERNG EDYICPNCTI L

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Dido_PHD	natural abundance	0.6 mM
2	potassium phosphate	natural abundance	10 uM
3	TCEP	natural abundance	100 uM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	DSS	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Dido_PHD	[U-99% 13C; U-99% 15N]	0.4 mM
8	potassium phosphate	natural abundance	10 uM
9	TCEP	natural abundance	100 uM
10	sodium azide	natural abundance	0.01 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %
13	DSS	natural abundance	10 uM

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 79.1 %, Completeness (bb): 72.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.1 % (1091 of 1380)	97.0 % (702 of 724)	59.9 % (315 of 526)	56.9 % (74 of 130)
Backbone	72.1 % (519 of 720)	96.8 % (240 of 248)	59.6 % (212 of 356)	57.8 % (67 of 116)
Sidechain	82.9 % (640 of 772)	97.1 % (462 of 476)	60.6 % (171 of 282)	50.0 % (7 of 14)
Aromatic	71.4 % (80 of 112)	92.9 % (52 of 56)	50.0 % (27 of 54)	50.0 % (1 of 2)
Methyl	81.5 % (75 of 92)	95.7 % (44 of 46)	67.4 % (31 of 46)

1. Dido PHD

GSMDPNALYC ICRQPHNNRF MICCDRCEEW FHGDCVGISE ARGRLLERNG EDYICPNCTI L

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Dido_PHD	natural abundance	0.6 mM
2	potassium phosphate	natural abundance	10 uM
3	TCEP	natural abundance	100 uM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	DSS	natural abundance	10 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Dido_PHD	[U-99% 13C; U-99% 15N]	0.4 mM
8	potassium phosphate	natural abundance	10 uM
9	TCEP	natural abundance	100 uM
10	sodium azide	natural abundance	0.01 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %
13	DSS	natural abundance	10 uM

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: -0.26 ppm, Outliers: 1 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: -0.26 ppm, Outliers: 1 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: -0.01 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: 0.19 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M3H, Strand ID: A Detail

Release date

2013-08-04

Citation

NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3
Santiveri, C.M., Garcia-Mayoral, M.F., Perez-Canadillas, J.M., Jimenez, M.
J. Biomol. NMR (2013), 56, 183-190, PubMed 23579637 , DOI 10.1007/s10858-013-9726-x , Abstract

Related entities 1. Dido PHD, : 1 : 7 : 163 entities Detail

Interaction partners 1. Dido PHD, : 17 interactors Detail

More details for 17 interactors identified by 11 citations

Experiments performed 14 experiments Detail

1 2D 1H-1H TOCSY