BMRB Entry 10035

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PDB ID: 1wk1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10035
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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 Lectin C-type domain derived from a hypothetical protein from C. elegans

Deposition date:

2006-11-01

Original release date:

2008-08-13

Authors:

Kobayashi, N.; Koshiba, S.; Inoue, M.; Tochio, N.; Kigawa, T.; Yokoyama, S.

Citation:

Citation: Kobayashi, N.; Koshiba, S.; Inoue, M.; Tochio, N.; Kigawa, T.; Yokoyama, S.. "Solution structure of Lectin C-type domain derived from a hypothetical protein from C. elegans" .

Assembly members:

Assembly members:
Lectin C-type homologue domain, polymer, 150 residues, Formula weight is not available

Natural source:

Natural source: Common Name: nematode Taxonomy ID: 6239 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source: Production method: cell free synthesis Vector: P030929-39

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Lectin C-type homologue domain: GSSGSSGVKFLTVNDDILSM PQARNFCASAGGYLADDLGD DKNNFYSSIAANTQFWIGLF KNSDGQFYWDRGQGINPDLL NQPITYWANGEPSNDPTRQC VYFDGRSGDKSKVWTTDTCA TPRPFICQKHRYDSDHKPNT IGDASGPSSG

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	633
15N chemical shifts	165
1H chemical shifts	962

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Hypothetical protein yk1067a12	1

Entities:

Entity 1, Hypothetical protein yk1067a12 150 residues - Formula weight is not available

1	GLY	SER	SER	GLY	SER	SER	GLY	VAL	LYS	PHE
2	LEU	THR	VAL	ASN	ASP	ASP	ILE	LEU	SER	MET
3	PRO	GLN	ALA	ARG	ASN	PHE	CYS	ALA	SER	ALA
4	GLY	GLY	TYR	LEU	ALA	ASP	ASP	LEU	GLY	ASP
5	ASP	LYS	ASN	ASN	PHE	TYR	SER	SER	ILE	ALA
6	ALA	ASN	THR	GLN	PHE	TRP	ILE	GLY	LEU	PHE
7	LYS	ASN	SER	ASP	GLY	GLN	PHE	TYR	TRP	ASP
8	ARG	GLY	GLN	GLY	ILE	ASN	PRO	ASP	LEU	LEU
9	ASN	GLN	PRO	ILE	THR	TYR	TRP	ALA	ASN	GLY
10	GLU	PRO	SER	ASN	ASP	PRO	THR	ARG	GLN	CYS
11	VAL	TYR	PHE	ASP	GLY	ARG	SER	GLY	ASP	LYS
12	SER	LYS	VAL	TRP	THR	THR	ASP	THR	CYS	ALA
13	THR	PRO	ARG	PRO	PHE	ILE	CYS	GLN	LYS	HIS
14	ARG	TYR	ASP	SER	ASP	HIS	LYS	PRO	ASN	THR
15	ILE	GLY	ASP	ALA	SER	GLY	PRO	SER	SER	GLY

Samples:

sample_1: Lectin C-type domain, [U-13C; U-15N], 0.89 mM; Phosphate 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 120 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	sample_1	not available	condition_1
3D 15N-separated NOESY	sample_1	not available	condition_1

Software:

xwinnmr v2.6, Bruker - collection

NMRPipe v20020425, Delaglio, F. - processing

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

Kujira v0.901, Kobayashi, N. - data analysis

CYANA v2.0.17, Guentert, P. - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 800 MHz

1	GLY	SER	SER	GLY	SER	SER	GLY	VAL	LYS	PHE
2	LEU	THR	VAL	ASN	ASP	ASP	ILE	LEU	SER	MET
3	PRO	GLN	ALA	ARG	ASN	PHE	CYS	ALA	SER	ALA
4	GLY	GLY	TYR	LEU	ALA	ASP	ASP	LEU	GLY	ASP
5	ASP	LYS	ASN	ASN	PHE	TYR	SER	SER	ILE	ALA
6	ALA	ASN	THR	GLN	PHE	TRP	ILE	GLY	LEU	PHE
7	LYS	ASN	SER	ASP	GLY	GLN	PHE	TYR	TRP	ASP
8	ARG	GLY	GLN	GLY	ILE	ASN	PRO	ASP	LEU	LEU
9	ASN	GLN	PRO	ILE	THR	TYR	TRP	ALA	ASN	GLY
10	GLU	PRO	SER	ASN	ASP	PRO	THR	ARG	GLN	CYS
11	VAL	TYR	PHE	ASP	GLY	ARG	SER	GLY	ASP	LYS
12	SER	LYS	VAL	TRP	THR	THR	ASP	THR	CYS	ALA
13	THR	PRO	ARG	PRO	PHE	ILE	CYS	GLN	LYS	HIS
14	ARG	TYR	ASP	SER	ASP	HIS	LYS	PRO	ASN	THR
15	ILE	GLY	ASP	ALA	SER	GLY	PRO	SER	SER	GLY

1	GLY	SER	SER	GLY	SER	SER	GLY	VAL	LYS	PHE
2	LEU	THR	VAL	ASN	ASP	ASP	ILE	LEU	SER	MET
3	PRO	GLN	ALA	ARG	ASN	PHE	CYS	ALA	SER	ALA
4	GLY	GLY	TYR	LEU	ALA	ASP	ASP	LEU	GLY	ASP
5	ASP	LYS	ASN	ASN	PHE	TYR	SER	SER	ILE	ALA
6	ALA	ASN	THR	GLN	PHE	TRP	ILE	GLY	LEU	PHE
7	LYS	ASN	SER	ASP	GLY	GLN	PHE	TYR	TRP	ASP
8	ARG	GLY	GLN	GLY	ILE	ASN	PRO	ASP	LEU	LEU
9	ASN	GLN	PRO	ILE	THR	TYR	TRP	ALA	ASN	GLY
10	GLU	PRO	SER	ASN	ASP	PRO	THR	ARG	GLN	CYS
11	VAL	TYR	PHE	ASP	GLY	ARG	SER	GLY	ASP	LYS
12	SER	LYS	VAL	TRP	THR	THR	ASP	THR	CYS	ALA
13	THR	PRO	ARG	PRO	PHE	ILE	CYS	GLN	LYS	HIS
14	ARG	TYR	ASP	SER	ASP	HIS	LYS	PRO	ASN	THR
15	ILE	GLY	ASP	ALA	SER	GLY	PRO	SER	SER	GLY