BMRB Entry 18855

Name: Backbone assignments of 8M urea denatured YibK from Haemophilus influenzae (HI0766)
Published: 2014-02-14

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18855

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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:

Backbone assignments of 8M urea denatured YibK from Haemophilus influenzae (HI0766)

Deposition date:

2012-11-24

Original release date:

2014-02-14

Authors:

Hsieh, Shu-Ju Micky; Hsu, Shang-Te Danny

Citation:

Citation: Hsieh, Shu-Ju Micky; Mallam, Anna; Jackson, Sophie; Hsu, Shang-Te Danny. "Backbone 1H, 13C and 15N assignments of YibK and avariant containing a unique cysteine residue at C-terminus in 8 M urea-denatured states" Biomol. NMR Assignments 8, 439-442 (2014).
PubMed: 23853076

Assembly members:

Assembly members:
YibK, polymer, 160 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Haemophilus influenzae Taxonomy ID: 727 Superkingdom: Bacteria Kingdom: not available Genus/species: Haemophilus influenzae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: Pet 17b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YibK: MLDIVLYEPEIPQNTGNIIR LCANTGFRLHLIEPLGFTWD DKRLRRSGLDYHEFAEIKRH KTFEAFLESEKPKRLFALTT KGCPAHSQVKFKLGDYLMFG PETRGIPMSILNEMPMEQKI RIPMTANSRSMNLSNSVAVT VYEAWRQLGYKGAVNLPEVK

Data sets:

assigned_chemical_shifts
- YibK_wt_in_denatured_state

Data type	Count
13C chemical shifts	444
15N chemical shifts	146
1H chemical shifts	146

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YibK	1

Entities:

Entity 1, YibK 160 residues - Formula weight is not available

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

Samples:

YibK_in_denatured_state: YibK, [U-13C; U-15N], 350 uM; D2O 10%; TRIS 50 mM; potassium chloride 200 mM; glycerol 10%; urea 7.2 M; H2O 90%

SEC-urea: pH: 7.5; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	YibK_in_denatured_state	isotropic	SEC-urea
3D CBCA(CO)NH	YibK_in_denatured_state	isotropic	SEC-urea
3D HNCO	YibK_in_denatured_state	isotropic	SEC-urea
3D HNCACB	YibK_in_denatured_state	isotropic	SEC-urea
3D HNCA	YibK_in_denatured_state	isotropic	SEC-urea
3D C(CO)NH	YibK_in_denatured_state	isotropic	SEC-urea

Software:

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection, data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker Avance 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

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

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

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