BMRB: 10098

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta

Authors

Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

Diacylglycerol kinase, delta

Entity

1. C1 Domain (polymer, Thiol state: free and other bound), 84 monomers, 8816.023 Da Detail

GSSGSSGTTL ASIGKDIIED ADGIAMPHQW LEGNLPVSAK CTVCDKTCGS VLRLQDWRCL WCKAMVHTSC KESLLTKCSG PSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8946.842 Da

Max. entity weight

8816.023 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS28:ND1	2:ZN1:ZN
2	na	sing	1:CYS59:SG	2:ZN1:ZN
3	na	sing	1:CYS62:SG	2:ZN1:ZN
4	na	sing	1:CYS78:SG	2:ZN1:ZN
5	na	sing	1:CYS41:SG	2:ZN1:ZN
6	na	sing	1:CYS44:SG	2:ZN1:ZN
7	na	sing	1:HIS67:ND1	2:ZN1:ZN
8	na	sing	1:CYS70:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.7 %, Completeness: 92.0 %, Completeness (bb): 88.6 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	92.0 % (825 of 897)	92.0 % (424 of 461)	92.6 % (323 of 349)	89.7 % (78 of 87)
Backbone	88.6 % (441 of 498)	86.8 % (151 of 174)	89.7 % (218 of 243)	88.9 % (72 of 81)
Sidechain	95.6 % (453 of 474)	95.1 % (273 of 287)	96.1 % (174 of 181)	100.0 % (6 of 6)
Aromatic	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (19 of 19)	100.0 % (3 of 3)
Methyl	97.7 % (84 of 86)	97.7 % (42 of 43)	97.7 % (42 of 43)

1. C1 Domain

GSSGSSGTTL ASIGKDIIED ADGIAMPHQW LEGNLPVSAK CTVCDKTCGS VLRLQDWRCL WCKAMVHTSC KESLLTKCSG PSSG

Show sample condition

Sample

Pressure 1 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	C1 Domain	[U-13C; U-15N]		1.05 mM
2	d-Tris-HCl		buffer	20 mM
3	NaCl		salt	100 mM
4	NaN3			0.02 %
5	ZnCl2			100 uM
6	H2O		solvent	90 %
7	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.11 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

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: -0.11 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

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: 0.0 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

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: 0.48 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

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: 1R79, Strand ID: A Detail

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Release date

2008-08-14

Citation

Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta
Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Related entities 1. C1 Domain, : 1 : 2 : 26 entities Detail

Interaction partners 1. C1 Domain, : 11 interactors Detail

Experiments performed 2 experiments Detail