BMRB: 11098

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

Authors

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

Assembly

Netrin receptor DCC

Entity

1. Netrin receptor DCC (polymer, Thiol state: all free), 114 monomers, 12497.13 Da Detail

GSSGSSGPTS APKDLTVITR EGKPRAVIVS WQPPLEANGK ITAYILFYTL DKNIPIDDWI METISGDRLT HQIMDLNLDT MYYFRIQARN SKGVGPLSDP ILFRTLKVSG PSSG

Formula weight

12497.13 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 97.1 %, Completeness (bb): 97.1 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	97.1 % (1275 of 1313)	96.2 % (656 of 682)	98.5 % (509 of 517)	96.5 % (110 of 114)
Backbone	97.1 % (647 of 666)	95.6 % (219 of 229)	98.5 % (327 of 332)	96.2 % (101 of 105)
Sidechain	97.5 % (732 of 751)	96.5 % (437 of 453)	99.0 % (286 of 289)	100.0 % (9 of 9)
Aromatic	97.8 % (88 of 90)	100.0 % (45 of 45)	95.3 % (41 of 43)	100.0 % (2 of 2)
Methyl	98.5 % (130 of 132)	98.5 % (65 of 66)	98.5 % (65 of 66)

1. sixth fn3 domain

GSSGSSGPTS APKDLTVITR EGKPRAVIVS WQPPLEANGK ITAYILFYTL DKNIPIDDWI METISGDRLT HQIMDLNLDT MYYFRIQARN SKGVGPLSDP ILFRTLKVSG 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 1.3mM sample [U-15N,13C]; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	sixth fn3 domain	[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: 0.07 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; CB

Referencing offset: 0.07 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; HA

Referencing offset: -0.03 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: 0.87 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: 2EDE, Strand ID: A Detail

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Release date

2011-02-16

Citation

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

Related entities 1. Netrin receptor DCC, : 1 : 484 entities Detail

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

Experiments performed 2 experiments Detail