BMRB: 11331

Solution structure of the B-box domain of the human Midline-2 protein

Authors

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

Assembly

Midline-2

Entity

1. zf-B box (polymer, Thiol state: all other bound), 84 monomers, 9181.261 Da Detail

GSSGSSGVEP VPDTHLRGIT CLDHENEKVN MYCVSDDQLI CALCKLVGRH RDHQVASLND RFEKLKQTLE MNLTNLVKSG PSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

9312.079 Da

Max. entity weight

9181.261 Da

Entity Connection

na 9 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS24:ND1	2:ZN1:ZN
2	na	sing	1:CYS21:SG	2:ZN1:ZN
3	na	sing	1:CYS41:SG	2:ZN1:ZN
4	na	sing	1:CYS44:SG	2:ZN1:ZN
5	na	sing	1:CYS33:SG	2:ZN1:ZN
6	na	sing	1:ASP36:OD1	2:ZN1:ZN
7	na	sing	1:HIS50:ND1	2:ZN1:ZN
8	na	sing	1:HIS53:ND1	2:ZN1:ZN
9	na	sing	1:ASP36:OD2	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: 92.9 %, Completeness: 92.2 %, Completeness (bb): 89.4 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	92.2 % (857 of 930)	91.9 % (445 of 484)	92.4 % (330 of 357)	92.1 % (82 of 89)
Backbone	89.4 % (445 of 498)	87.8 % (151 of 172)	89.8 % (220 of 245)	91.4 % (74 of 81)
Sidechain	95.1 % (484 of 509)	94.2 % (294 of 312)	96.3 % (182 of 189)	100.0 % (8 of 8)
Aromatic	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. zf-B box

GSSGSSGVEP VPDTHLRGIT CLDHENEKVN MYCVSDDQLI CALCKLVGRH RDHQVASLND RFEKLKQTLE MNLTNLVKSG PSSG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05), Details 1.92mM zf-B_box {U-13C,15N;} 20mM {d-Tris-HCl(pH7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 0.05mM {ZNCl2;} 1.0mM {IDA;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	zf-B box	[U-13C; U-15N]	protein	1.92 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	ZnCl2	natural abundance	salt	0.05 mM
7	IDA	natural abundance	salt	1.0 mM
8	H2O		solvent	90 %
9	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: 0.0 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
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: 0.0 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
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: 0.01 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
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.1 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
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

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

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Release date

2011-08-18

Citation

Solution structure of the B-box domain of the human Midline-2 protein
Miyamoto, K., Kigawa, T., Tomizawa, T., Koshiba, S., Inoue, M., Yokoyama, S.

Related entities 1. zf-B box, : 1 : 5 : 54 entities Detail

Interaction partners 1. zf-B box, : 117 interactors Detail

Experiments performed 2 experiments Detail