BMRB: 11097

Solution structure of the fifth 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), 123 monomers, 13218.52 Da Detail

GSSGSSGFPT SVPDLSTPML PPVGVQAVAL THDAVRVSWA DNSVPKNQKT SEVRLYTVRW RTSFSASAKY KSEDTTSLSY TATGLKPNTM YEFSVMVTKN RRSSTWSMTA HATTYEASGP SSG

Formula weight

13218.52 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.1 %, Completeness: 92.2 %, Completeness (bb): 92.1 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	92.2 % (1238 of 1343)	90.8 % (624 of 687)	94.2 % (501 of 532)	91.1 % (113 of 124)
Backbone	92.1 % (665 of 722)	90.2 % (221 of 245)	93.9 % (340 of 362)	90.4 % (104 of 115)
Sidechain	92.8 % (684 of 737)	91.2 % (403 of 442)	95.1 % (272 of 286)	100.0 % (9 of 9)
Aromatic	87.7 % (100 of 114)	87.7 % (50 of 57)	87.0 % (47 of 54)	100.0 % (3 of 3)
Methyl	96.7 % (116 of 120)	96.7 % (58 of 60)	96.7 % (58 of 60)

1. fifth fn3 domain

GSSGSSGFPT SVPDLSTPML PPVGVQAVAL THDAVRVSWA DNSVPKNQKT SEVRLYTVRW RTSFSASAKY KSEDTTSLSY TATGLKPNTM YEFSVMVTKN RRSSTWSMTA HATTYEASGP SSG

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Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05), Details 1.2mM 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	fifth fn3 domain	[U-13C; U-15N]	protein	1.2 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: -0.05 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: -0.05 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: 0.02 ppm, Outliers: 5 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: 0.62 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: 2EDD, Strand ID: A Detail

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Release date

2011-02-16

Related entities 1. Netrin receptor DCC, : 1 : 83 entities Detail

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

Experiments performed 2 experiments Detail