BMRB: 11353

Solution structure of PHD domain in inhibitor of growth protein 3 (ING3)

Authors

He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S.

Assembly

Inhibitor of growth protein 3

Entity

1. PHD domain (polymer, Thiol state: all other bound), 70 monomers, 7512.357 Da Detail

GSSGSSGYCI CNQVSYGEMV GCDNQDCPIE WFHYGCVGLT EAPKGKWYCP QCTAAMKRRG SRHKSGPSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

7643.175 Da

Max. entity weight

7512.357 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS9:SG	2:ZN1:ZN
2	na	sing	1:CYS11:SG	2:ZN1:ZN
3	na	sing	1:HIS33:ND1	2:ZN1:ZN
4	na	sing	1:CYS36:SG	2:ZN1:ZN
5	na	sing	1:CYS22:SG	2:ZN1:ZN
6	na	sing	1:CYS27:SG	2:ZN1:ZN
7	na	sing	1:CYS49:SG	2:ZN1:ZN
8	na	sing	1:CYS52:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

Torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 93.5 %, Completeness (bb): 90.8 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	93.5 % (705 of 754)	92.9 % (366 of 394)	95.5 % (274 of 287)	89.0 % (65 of 73)
Backbone	90.8 % (374 of 412)	88.4 % (130 of 147)	93.5 % (186 of 199)	87.9 % (58 of 66)
Sidechain	96.5 % (387 of 401)	95.5 % (236 of 247)	98.0 % (144 of 147)	100.0 % (7 of 7)
Aromatic	100.0 % (74 of 74)	100.0 % (37 of 37)	100.0 % (35 of 35)	100.0 % (2 of 2)
Methyl	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)

1. PHD domain

GSSGSSGYCI CNQVSYGEMV GCDNQDCPIE WFHYGCVGLT EAPKGKWYCP QCTAAMKRRG SRHKSGPSSG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.05), Details 0.8mM {U-15,13C;} 20mM d-Tris-HCl(pH {7.0);} 100mM {NaCl;} 0.1mM {ZnCl2;} 1mM {d-DTT;} 0.02% NaN3

#	Name	Isotope labeling	Type	Concentration
1	PHD domain	[U-13C; U-15N]	protein	0.8 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	ZnCl2	natural abundance	salt	0.1 mM
5	d-DTT	natural abundance	salt	1 mM
6	NaN3	natural abundance	salt	0.02 %
7	H2O		solvent	90 %
8	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.09 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.09 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.01 ppm, Outliers: 4 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 1X4I, Strand ID: A Detail

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Release date

2011-09-06

Citation

Solution structure of PHD domain in inhibitor of growth protein 3 (ING3)
He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S.

Related entities 1. PHD domain, : 1 : 5 : 45 entities Detail

Interaction partners 1. PHD domain, : 7 interactors Detail

Experiments performed 2 experiments Detail