BMRB: 11096

Solution structure of the first fibronectin type III domain of human Netrin receptor DCC

Authors

Tochio, N., Koshiba, S., Tomizawa, T., Kigawa, T., Yokoyama, S.

Assembly

Netrin receptor DCC

Entity

1. Netrin receptor DCC (polymer, Thiol state: all free), 119 monomers, 12646.97 Da Detail

GSSGSSGKPA IPSSSVLPSA PRDVVPVLVS SRFVRLSWRP PAEAKGNIQT FTVFFSREGD NRERALNTTQ PGSLQLTVGN LKPEAMYTFR VVAYNEWGPG ESSQPIKVAT QPESGPSSG

Formula weight

12646.97 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.3 %, Completeness: 90.9 %, Completeness (bb): 90.1 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	90.9 % (1206 of 1327)	90.3 % (626 of 693)	92.2 % (476 of 516)	88.1 % (104 of 118)
Backbone	90.1 % (620 of 688)	90.3 % (213 of 236)	90.8 % (314 of 346)	87.7 % (93 of 106)
Sidechain	91.8 % (686 of 747)	90.4 % (413 of 457)	94.2 % (262 of 278)	91.7 % (11 of 12)
Aromatic	94.4 % (85 of 90)	95.6 % (43 of 45)	95.3 % (41 of 43)	50.0 % (1 of 2)
Methyl	100.0 % (114 of 114)	100.0 % (57 of 57)	100.0 % (57 of 57)

1. first fn3 domain, Fibronectin type-III 1

GSSGSSGKPA IPSSSVLPSA PRDVVPVLVS SRFVRLSWRP PAEAKGNIQT FTVFFSREGD NRERALNTTQ PGSLQLTVGN LKPEAMYTFR VVAYNEWGPG ESSQPIKVAT QPESGPSSG

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Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.05), Details 1.3mM sample [U-15N,13C]; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O

#	Name	Isotope labeling	Type	Concentration
1	first fn3 domain, Fibronectin type-III 1	[U-13C; U-15N]	protein	1.3 mM
2	d-Tris-HCl	[U-2H]	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	d-DTT	[U-2H]	salt	1 mM
5	sodium azide	natural abundance	salt	0.02 %
6	H2O		solvent	90 %
7	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: 0.13 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: 0.13 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: 0.02 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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LACS Plot; CO

Referencing offset: 0.6 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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Protein Blocks Logo

Calculated from 20 models in PDB: 2ED7, Strand ID: A Detail

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Release date

2011-02-16

Citation

Solution structure of the first fibronectin type III domain of human Netrin receptor DCC
Tochio, N., Koshiba, S., Tomizawa, T., Kigawa, T., Yokoyama, S.

Related entities 1. Netrin receptor DCC, : 1 : 2 : 357 entities Detail

Interaction partners 1. Netrin receptor DCC, : 24 interactors Detail

Experiments performed 2 experiments Detail