BMRB Entry 11099

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PDB ID: 2edb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11099
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2010-02-18

Original release date:

2011-02-17

Authors:

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

Citation:

Citation: Tochio, N.; Koshiba, S.; Kigawa, T.; Yokoyama, S.. "Solution structure of the fourth fibronectin type III domain of human Netrin receptor DCC" .

Assembly members:

Assembly members:
fourth fn3 domain, polymer, 116 residues, Formula weight is not available

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: E. coli - cell free Vector: P050905-22

Entity Sequences (FASTA):

Entity Sequences (FASTA):
fourth fn3 domain: GSSGSSGPENDLDESQVPDQ PSSLHVRPQTNCIIMSWTPP LNPNIVVRGYIIGYGVGSPY AETVRVDSKQRYYSIERLES SSHYVISLKAFNNAGEGVPL YESATTRSITSGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	467
15N chemical shifts	108
1H chemical shifts	716

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	fourth fn3 domain	1

Entities:

Entity 1, fourth fn3 domain 116 residues - Formula weight is not available

1

GLY

SER

GLY

SER

GLY

PRO

GLU

ASN

2

ASP

LEU

ASP

GLU

SER

GLN

VAL

PRO

ASP

GLN

3

PRO

SER

LEU

HIS

VAL

ARG

PRO

GLN

THR

4

ASN

CYS

ILE

MET

SER

TRP

THR

PRO

5

LEU

ASN

PRO

ASN

ILE

VAL

ARG

GLY

TYR

6

ILE

GLY

TYR

GLY

VAL

GLY

SER

PRO

TYR

7

ALA

GLU

THR

VAL

ARG

VAL

ASP

SER

LYS

GLN

8

ARG

TYR

SER

ILE

GLU

ARG

LEU

GLU

SER

9

SER

HIS

TYR

VAL

ILE

SER

LEU

LYS

ALA

10

PHE

ASN

ALA

GLY

GLU

GLY

VAL

PRO

LEU

11

TYR

GLU

SER

ALA

THR

ARG

SER

ILE

THR

12

SER

GLY

PRO

SER

GLY

Samples:

sample_1: fourth fn3 domain, [U-13C; U-15N], 1.2 mM; d-Tris-HCl, [U-2H], 20 mM; sodium chloride 100 mM; d-DTT, [U-2H], 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	condition_1
3D 1H-13C NOESY	sample_1	isotropic	condition_1

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20031121, Delaglio, F. - processing

NMNMRView v5.0.4, Johnson, B.A. - data analysis

Kujira v0.955, Kobayashi, N. - data analysis

CYANA v2.0.17, Guntert, P. - structure solution

NMR spectrometers:

Bruker AVANCE 900 MHz

PDB	2EDB 4PLO
DBJ	BAG63884 BAI45499
EMBL	CAA53735
GB	AAH36524 AAI52809 EAW62991 EAW62994 EFB26812
REF	NP_005206 XP_001916613 XP_002757292 XP_002800982 XP_002828277
SP	P43146
TPG	DAA15913
AlphaFold	P43146