BMRB: 11354

Solution structure of PHD domain in ING1-like protein BAC25079

Authors

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

Assembly

inhibitor of growth family, member 4 ING1-like protein

Entity

1. PHD domain (polymer, Thiol state: all other bound), 71 monomers, 7635.413 Da Detail

GSSGSSGDMP VDPNEPTYCL CHQVSYGEMI GCDNPDCSIE WFHFACVGLT TKPRGKWFCP RCSQESGPSS G

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

7766.231 Da

Max. entity weight

7635.413 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS46:SG	2:ZN1:ZN
2	na	sing	1:CYS19:SG	2:ZN1:ZN
3	na	sing	1:HIS43:ND1	2:ZN1:ZN
4	na	sing	1:CYS21:SG	2:ZN1:ZN
5	na	sing	1:CYS37:SG	2:ZN1:ZN
6	na	sing	1:CYS32:SG	2:ZN1:ZN
7	na	sing	1:CYS59:SG	2:ZN1:ZN
8	na	sing	1:CYS62:SG	2:ZN1:ZN

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

Torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 96.3 %, Completeness (bb): 94.9 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	96.3 % (735 of 763)	96.0 % (381 of 397)	97.3 % (288 of 296)	94.3 % (66 of 70)
Backbone	94.9 % (391 of 412)	93.8 % (135 of 144)	96.1 % (196 of 204)	93.8 % (60 of 64)
Sidechain	97.8 % (404 of 413)	97.2 % (246 of 253)	98.7 % (152 of 154)	100.0 % (6 of 6)
Aromatic	100.0 % (78 of 78)	100.0 % (39 of 39)	100.0 % (37 of 37)	100.0 % (2 of 2)
Methyl	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)

1. PHD domain

GSSGSSGDMP VDPNEPTYCL CHQVSYGEMI GCDNPDCSIE WFHFACVGLT TKPRGKWFCP RCSQESGPSS G

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 293 (±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-TDD;} 0.02% {NaN3;} 90% H2O, 10% D2O

#	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: -0.29 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: -0.29 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: -0.04 ppm, Outliers: 2 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: 0.06 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: 1WEN, Strand ID: A Detail

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Release date

2011-09-06

Citation

Solution structure of PHD domain in ING1-like protein BAC25079
He, F., Muto, Y., Inoue, M., Kigawa, T., Shirouzu, M., Terada, T., Yokoyama, S.

Related entities 1. PHD domain, : 1 : 10 : 68 entities Detail

Interaction partners 1. PHD domain, : 2 interactors Detail

Experiments performed 2 experiments Detail