BMRB Entry 18609

Name: Chemical shifts of Ecoli GGBP sugar bound
Published: 2014-04-22

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR18609

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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:

Chemical shifts of Ecoli GGBP sugar bound

Deposition date:

2012-07-23

Original release date:

2014-04-22

Authors:

Millet, Oscar; Castano, David; Ortega, Gabriel; Diercks, Tammo

Citation:

Citation: Ortega, Gabriel; Castano, David; Diercks, Tammo; Millet, Oscar. "Carbohydrate affinity for the glucose-galactose binding protein is regulated by allosteric domain motions." J. Am. Chem. Soc. 134, 19869-19876 (2012).
PubMed: 23148479

Assembly members:

Assembly members:
GGBP, polymer, 310 residues, 30000 Da.
BETA-D-GLUCOSE, non-polymer, 180.156 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11-d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GGBP: MADTRIGVTIYKYDDNFMSV VRKAIEQDAKAAPDVQLLMN DSQNDQSKQNDQIDVLLAKG VKALAINLVDPAAAGTVIEK ARGQNVPVVFFNKEPSRKAL DSYDKAYYVGTDSKESGIIQ GDLIAKHWAANQGWDLNKDG QIQFVLLKGEPGHPDAEART TYVIKELNDKGIKTEQLQLD TAMWDTAQAKDKMDAWLSGP NANKIEVVIANNDAMAMGAV EALKAHNKSSIPVFGVDALP EALALVKSGALAGTVLNDAN NQAKATFDLAKNLADGKGAA DGTNWKIDNKVVRVPYVGVD KDNLAEFSKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	495
15N chemical shifts	257
1H chemical shifts	257

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	GGBP	1
2	Glucose	2

Entities:

Entity 1, GGBP 310 residues - 30000 Da.

1	MET	ALA	ASP	THR	ARG	ILE	GLY	VAL	THR	ILE
2	TYR	LYS	TYR	ASP	ASP	ASN	PHE	MET	SER	VAL
3	VAL	ARG	LYS	ALA	ILE	GLU	GLN	ASP	ALA	LYS
4	ALA	ALA	PRO	ASP	VAL	GLN	LEU	LEU	MET	ASN
5	ASP	SER	GLN	ASN	ASP	GLN	SER	LYS	GLN	ASN
6	ASP	GLN	ILE	ASP	VAL	LEU	LEU	ALA	LYS	GLY
7	VAL	LYS	ALA	LEU	ALA	ILE	ASN	LEU	VAL	ASP
8	PRO	ALA	ALA	ALA	GLY	THR	VAL	ILE	GLU	LYS
9	ALA	ARG	GLY	GLN	ASN	VAL	PRO	VAL	VAL	PHE
10	PHE	ASN	LYS	GLU	PRO	SER	ARG	LYS	ALA	LEU
11	ASP	SER	TYR	ASP	LYS	ALA	TYR	TYR	VAL	GLY
12	THR	ASP	SER	LYS	GLU	SER	GLY	ILE	ILE	GLN
13	GLY	ASP	LEU	ILE	ALA	LYS	HIS	TRP	ALA	ALA
14	ASN	GLN	GLY	TRP	ASP	LEU	ASN	LYS	ASP	GLY
15	GLN	ILE	GLN	PHE	VAL	LEU	LEU	LYS	GLY	GLU
16	PRO	GLY	HIS	PRO	ASP	ALA	GLU	ALA	ARG	THR
17	THR	TYR	VAL	ILE	LYS	GLU	LEU	ASN	ASP	LYS
18	GLY	ILE	LYS	THR	GLU	GLN	LEU	GLN	LEU	ASP
19	THR	ALA	MET	TRP	ASP	THR	ALA	GLN	ALA	LYS
20	ASP	LYS	MET	ASP	ALA	TRP	LEU	SER	GLY	PRO
21	ASN	ALA	ASN	LYS	ILE	GLU	VAL	VAL	ILE	ALA
22	ASN	ASN	ASP	ALA	MET	ALA	MET	GLY	ALA	VAL
23	GLU	ALA	LEU	LYS	ALA	HIS	ASN	LYS	SER	SER
24	ILE	PRO	VAL	PHE	GLY	VAL	ASP	ALA	LEU	PRO
25	GLU	ALA	LEU	ALA	LEU	VAL	LYS	SER	GLY	ALA
26	LEU	ALA	GLY	THR	VAL	LEU	ASN	ASP	ALA	ASN
27	ASN	GLN	ALA	LYS	ALA	THR	PHE	ASP	LEU	ALA
28	LYS	ASN	LEU	ALA	ASP	GLY	LYS	GLY	ALA	ALA
29	ASP	GLY	THR	ASN	TRP	LYS	ILE	ASP	ASN	LYS
30	VAL	VAL	ARG	VAL	PRO	TYR	VAL	GLY	VAL	ASP
31	LYS	ASP	ASN	LEU	ALA	GLU	PHE	SER	LYS	LYS

Entity 2, Glucose - C6 H12 O6 - 180.156 Da.

1

BGC

Samples:

sample_assi: Glucose 3 mM; GGBP, [U-13C; U-15N; U-2H], 1 mM; sodium azide 1 mM; sodium chloride 150 mM; TRIS 20 mM; H2O 90%; H2O 10%

sample_conditions_1: ionic strength: 0.15 M; pH: 7; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_assi	isotropic	sample_conditions_1
3D HNCO	sample_assi	isotropic	sample_conditions_1
3D HNCA	sample_assi	isotropic	sample_conditions_1
3D HN(CO)CA	sample_assi	isotropic	sample_conditions_1
3D HNCB	sample_assi	isotropic	sample_conditions_1
3D HN(CO)CB	sample_assi	isotropic	sample_conditions_1

Software:

TOPSPIN v2, Bruker Biospin - collection

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

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, peak picking

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker INOVA 800 MHz

BMRB	18601
PDB	1GLG 2FVY 2FW0 2GBP 2HPH 2IPL 2IPM 2IPN 2QW1
DBJ	BAB36465 BAE76627 BAG77941 BAI26274 BAI31400
EMBL	CAA29132 CAP76652 CAQ89737 CAQ99072 CAR03578
GB	AAA24169 AAA60523 AAC75211 AAG57288 AAN43756
PRF	2014253AU
REF	NP_311069 NP_416655 NP_708049 WP_001035789 WP_001036935
SP	P0AEE5 P0AEE6 P0AEE7
AlphaFold	P0AEE7 P0AEE5 P0AEE6

1	MET	ALA	ASP	THR	ARG	ILE	GLY	VAL	THR	ILE
2	TYR	LYS	TYR	ASP	ASP	ASN	PHE	MET	SER	VAL
3	VAL	ARG	LYS	ALA	ILE	GLU	GLN	ASP	ALA	LYS
4	ALA	ALA	PRO	ASP	VAL	GLN	LEU	LEU	MET	ASN
5	ASP	SER	GLN	ASN	ASP	GLN	SER	LYS	GLN	ASN
6	ASP	GLN	ILE	ASP	VAL	LEU	LEU	ALA	LYS	GLY
7	VAL	LYS	ALA	LEU	ALA	ILE	ASN	LEU	VAL	ASP
8	PRO	ALA	ALA	ALA	GLY	THR	VAL	ILE	GLU	LYS
9	ALA	ARG	GLY	GLN	ASN	VAL	PRO	VAL	VAL	PHE
10	PHE	ASN	LYS	GLU	PRO	SER	ARG	LYS	ALA	LEU
11	ASP	SER	TYR	ASP	LYS	ALA	TYR	TYR	VAL	GLY
12	THR	ASP	SER	LYS	GLU	SER	GLY	ILE	ILE	GLN
13	GLY	ASP	LEU	ILE	ALA	LYS	HIS	TRP	ALA	ALA
14	ASN	GLN	GLY	TRP	ASP	LEU	ASN	LYS	ASP	GLY
15	GLN	ILE	GLN	PHE	VAL	LEU	LEU	LYS	GLY	GLU
16	PRO	GLY	HIS	PRO	ASP	ALA	GLU	ALA	ARG	THR
17	THR	TYR	VAL	ILE	LYS	GLU	LEU	ASN	ASP	LYS
18	GLY	ILE	LYS	THR	GLU	GLN	LEU	GLN	LEU	ASP
19	THR	ALA	MET	TRP	ASP	THR	ALA	GLN	ALA	LYS
20	ASP	LYS	MET	ASP	ALA	TRP	LEU	SER	GLY	PRO
21	ASN	ALA	ASN	LYS	ILE	GLU	VAL	VAL	ILE	ALA
22	ASN	ASN	ASP	ALA	MET	ALA	MET	GLY	ALA	VAL
23	GLU	ALA	LEU	LYS	ALA	HIS	ASN	LYS	SER	SER
24	ILE	PRO	VAL	PHE	GLY	VAL	ASP	ALA	LEU	PRO
25	GLU	ALA	LEU	ALA	LEU	VAL	LYS	SER	GLY	ALA
26	LEU	ALA	GLY	THR	VAL	LEU	ASN	ASP	ALA	ASN
27	ASN	GLN	ALA	LYS	ALA	THR	PHE	ASP	LEU	ALA
28	LYS	ASN	LEU	ALA	ASP	GLY	LYS	GLY	ALA	ALA
29	ASP	GLY	THR	ASN	TRP	LYS	ILE	ASP	ASN	LYS
30	VAL	VAL	ARG	VAL	PRO	TYR	VAL	GLY	VAL	ASP
31	LYS	ASP	ASN	LEU	ALA	GLU	PHE	SER	LYS	LYS

1	MET	ALA	ASP	THR	ARG	ILE	GLY	VAL	THR	ILE
2	TYR	LYS	TYR	ASP	ASP	ASN	PHE	MET	SER	VAL
3	VAL	ARG	LYS	ALA	ILE	GLU	GLN	ASP	ALA	LYS
4	ALA	ALA	PRO	ASP	VAL	GLN	LEU	LEU	MET	ASN
5	ASP	SER	GLN	ASN	ASP	GLN	SER	LYS	GLN	ASN
6	ASP	GLN	ILE	ASP	VAL	LEU	LEU	ALA	LYS	GLY
7	VAL	LYS	ALA	LEU	ALA	ILE	ASN	LEU	VAL	ASP
8	PRO	ALA	ALA	ALA	GLY	THR	VAL	ILE	GLU	LYS
9	ALA	ARG	GLY	GLN	ASN	VAL	PRO	VAL	VAL	PHE
10	PHE	ASN	LYS	GLU	PRO	SER	ARG	LYS	ALA	LEU
11	ASP	SER	TYR	ASP	LYS	ALA	TYR	TYR	VAL	GLY
12	THR	ASP	SER	LYS	GLU	SER	GLY	ILE	ILE	GLN
13	GLY	ASP	LEU	ILE	ALA	LYS	HIS	TRP	ALA	ALA
14	ASN	GLN	GLY	TRP	ASP	LEU	ASN	LYS	ASP	GLY
15	GLN	ILE	GLN	PHE	VAL	LEU	LEU	LYS	GLY	GLU
16	PRO	GLY	HIS	PRO	ASP	ALA	GLU	ALA	ARG	THR
17	THR	TYR	VAL	ILE	LYS	GLU	LEU	ASN	ASP	LYS
18	GLY	ILE	LYS	THR	GLU	GLN	LEU	GLN	LEU	ASP
19	THR	ALA	MET	TRP	ASP	THR	ALA	GLN	ALA	LYS
20	ASP	LYS	MET	ASP	ALA	TRP	LEU	SER	GLY	PRO
21	ASN	ALA	ASN	LYS	ILE	GLU	VAL	VAL	ILE	ALA
22	ASN	ASN	ASP	ALA	MET	ALA	MET	GLY	ALA	VAL
23	GLU	ALA	LEU	LYS	ALA	HIS	ASN	LYS	SER	SER
24	ILE	PRO	VAL	PHE	GLY	VAL	ASP	ALA	LEU	PRO
25	GLU	ALA	LEU	ALA	LEU	VAL	LYS	SER	GLY	ALA
26	LEU	ALA	GLY	THR	VAL	LEU	ASN	ASP	ALA	ASN
27	ASN	GLN	ALA	LYS	ALA	THR	PHE	ASP	LEU	ALA
28	LYS	ASN	LEU	ALA	ASP	GLY	LYS	GLY	ALA	ALA
29	ASP	GLY	THR	ASN	TRP	LYS	ILE	ASP	ASN	LYS
30	VAL	VAL	ARG	VAL	PRO	TYR	VAL	GLY	VAL	ASP
31	LYS	ASP	ASN	LEU	ALA	GLU	PHE	SER	LYS	LYS