BMRBj - BMREntryMaster

Found 1 Document (1.464 seconds)

BMRB: 7210

2K1J

plant homeodomain finger of the tumour suppressor ING4

Authors

Palacios, A., Garcia, P., Padro, D., Lopez-Hernandez, E., Blanco, F.

Assembly

Plant HomeoDomain of ING4

Entity

1. ING4 PHD (polymer, Thiol state: all other bound), 63 monomers, 7315.392 Da Detail

MDMPVDPNEP TYCLCHQVSY GEMIGCDNPD CSIEWFHFAC VGLTTKPRGK WFCPRCSQER KKK

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

7446.21 Da

Max. entity weight

7315.392 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS13:SG	2:ZN1:ZN
2	na	sing	1:CYS15:SG	2:ZN1:ZN
3	na	sing	1:HIS37:ND1	2:ZN1:ZN
4	na	sing	1:CYS40:SG	2:ZN1:ZN
5	na	sing	1:CYS26:SG	2:ZN1:ZN
6	na	sing	1:CYS31:SG	2:ZN1:ZN
7	na	sing	1:CYS53:SG	2:ZN1:ZN
8	na	sing	1:CYS56:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, coupling_constants

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 89.5 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.5 % (666 of 744)	90.1 % (354 of 393)	88.9 % (256 of 288)	88.9 % (56 of 63)
Backbone	94.8 % (347 of 366)	94.4 % (117 of 124)	94.1 % (174 of 185)	98.2 % (56 of 57)
Sidechain	86.3 % (377 of 437)	88.1 % (237 of 269)	86.4 % (140 of 162)	0.0 % (0 of 6)
Aromatic	71.8 % (56 of 78)	82.1 % (32 of 39)	64.9 % (24 of 37)	0.0 % (0 of 2)
Methyl	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)

1. ING4 PHD

MDMPVDPNEP TYCLCHQVSY GEMIGCDNPD CSIEWFHFAC VGLTTKPRGK WFCPRCSQER KKK

Show sample condition

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

LACS Plot; CA

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

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.14 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 2K1J, Strand ID: A Detail

Coupling constant

49 J values in 1 lists
Temperature 298 (±0.1) K, pH 6.5 (±0.1) Detail

Release date

2007-01-08

Citation

Solution structure and NMR characterization of the binding to methylated histone tails of the plant homeodomain finger of the tumour suppressor ING4
Palacios, A., Garcia, P., Padro, D., Lopez-Hernandez, E., Martin, I., Blanco, F.
FEBS Lett. (2006), 580, 6903-6908, PubMed 17157298 , DOI 10.1016/j.febslet.2006.11.055 , Abstract

Related entities 1. ING4 PHD, : 1 : 7 : 3 : 113 entities Detail

Interaction partners 1. ING4 PHD, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H15N_HSQC

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

2 2D 1H13C_HSQC

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

3 3D CBCA(CO)NH

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

4 3D HNCACB

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

5 3D (H)C(CCO)NH

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

6 3D HNHA

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

7 3D HNHB

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

8 3D 15N edited TOCSY

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

9 3D 15N edited NOESY

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

10 3D 13C edited NOESY

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

11 3D HCCH-TOCSY

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

12 3D HNCO

Instrument

#1 Model Bruker Avance (600 MHz)

#2 Model Bruker Avance (700 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ING4_PHD	[U-95% 13C; U-90% 15N]	protein	1.2 mM
2	sodium phosphate		buffer	20 mM
3	NaCl		salt	50 mM
4	DTT		reducing agent	1 mM
5	D2O			9 %

Sample #2

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
6	ING4_PHD	[U-95% 13C; U-90% 15N]	1.2 mM
7	sodium phosphate		20 mM
8	NaCl		50 mM
9	DTT		1 mM
10	D2O		100 %

Sample #3

Temperature 298 (±0.1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
11	ING4_PHD	[U-90% 15N]	0.9 mM
12	sodium phosphate		20 mM
13	NaCl		50 mM
14	DTT		1 mM
15	D2O		9 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr7210_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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:13:CYS:SG	2:1:ZN:ZN	reduced, CA 59.517, CB 30.312 ppm	unknown	n/a
1:15:CYS:SG	2:1:ZN:ZN	reduced, CA 57.996, CB 31.017 ppm	unknown	n/a
1:37:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:40:CYS:SG	2:1:ZN:ZN	reduced, CA 62.545, CB 30.522 ppm	unknown	n/a
1:26:CYS:SG	3:1:ZN:ZN	oxidized 3.7%, reduced 96.3%, CA 60.409, CB 32.091 ppm	unknown	n/a
1:31:CYS:SG	3:1:ZN:ZN	reduced, CA 62.986, CB 30.691 ppm	unknown	n/a
1:53:CYS:SG	3:1:ZN:ZN	reduced, CA 57.613, CB 30.395 ppm	unknown	n/a
1:56:CYS:SG	3:1:ZN:ZN	reduced, CA 63.918, CB 29.739 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr7210_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	715		98.4 (chain: 1, length: 63)
1	Chemical shift references	chemical_shift_referencing	OK	3		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 63, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 403
  - ¹³C chemical shifts: 256
  - ¹⁵N chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	393	363	92.4
¹³C chemical shifts	288	256	88.9
¹⁵N chemical shifts	66	56	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	121	97.6
¹³C chemical shifts	126	116	92.1
¹⁵N chemical shifts	57	56	98.2

Keywords ING4, PHD

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	269	242	90.0
¹³C chemical shifts	162	140	86.4
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	32	82.1
¹³C chemical shifts	37	24	64.9
¹⁵N chemical shifts	2	0	0.0

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Found 1 Document (1.464 seconds)

BMRB: 7210

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ING4 PHD, : 1 : 7 : 3 : 113 entities Detail

Interaction partners 1. ING4 PHD, : 2 interactors Detail

Experiments performed 12 experiments Detail

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