BMRB: 11279

2DZI/Solution Structure of the N-terminal Ubiquitin-like Domain in Human Ubiquitin-like Protein 4A (GDX)

Authors

Zhao, C., Sato, M., Koshiba, S., Watanabe, S., Harada, T., Kigawa, T., Yokoyama, S.

Assembly

Ubiquitin-like protein 4A

Entity

1. Ubiquitin-like protein 4A (polymer, Thiol state: all free), 81 monomers, 8750.067 Da Detail

GSSGSSGMQL TVKALQGREC SLQVPEDELV STLKQLVSEK LNVPVRQQRL LFKGKALADG KRLSDYSIGP NSKLNLVVKP L

Formula weight

8750.067 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, restrained molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 95.0 %, Completeness (bb): 93.3 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	95.0 % (896 of 943)	94.4 % (469 of 497)	96.4 % (347 of 360)	93.0 % (80 of 86)
Backbone	93.3 % (446 of 478)	92.1 % (152 of 165)	94.5 % (223 of 236)	92.2 % (71 of 77)
Sidechain	96.7 % (521 of 539)	95.5 % (317 of 332)	98.5 % (195 of 198)	100.0 % (9 of 9)
Aromatic	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)
Methyl	100.0 % (102 of 102)	100.0 % (51 of 51)	100.0 % (51 of 51)

1. ubiquitin-like domain

GSSGSSGMQL TVKALQGREC SLQVPEDELV STLKQLVSEK LNVPVRQQRL LFKGKALADG KRLSDYSIGP NSKLNLVVKP L

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Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 296.0 (±0.1) K, pH 7.0 (±0.05), Details 1.18mM ubiquitin-like domain U-15N, {13C;} 20mM d-Tris-HCl (pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	ubiquitin-like domain	[U-13C; U-15N]	protein	1.18 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	H2O		solvent	90 %
7	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.26 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: -0.26 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: -0.11 ppm, Outliers: 3 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: 0.48 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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Protein Blocks Logo

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

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Release date

2011-08-17

Citation

2DZI/Solution Structure of the N-terminal Ubiquitin-like Domain in Human Ubiquitin-like Protein 4A (GDX)
Zhao, C., Sato, M., Koshiba, S., Watanabe, S., Harada, T., Kigawa, T., Yokoyama, S.

Related entities 1. Ubiquitin-like protein 4A, : 1 : 7 : 710 entities Detail

Interaction partners 1. Ubiquitin-like protein 4A, : 40 interactors Detail

Experiments performed 2 experiments Detail