BMRB Entry 51165

Name: Backbone assignment of Verona integron encoded metallo-beta-lactamase 2 (VIM-2)
Published: 2022-03-07

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51165

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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 assignment of Verona integron encoded metallo-beta-lactamase 2 (VIM-2)

Deposition date: 2021-11-02 Original release date: 2022-03-07

Authors: Wieske, Lianne; Bogaerts, Jonathan; Leding, Albin; Wilcox, Scott; Andersson Rasmussen, Anna; Leszczak, Kinga; Turunen, Lotta; Herrebout, Wouter; Hubert, Madlen; Bayer, Annette; Erdelyi, Mate

Citation: Wieske, Lianne; Bogaerts, Jonathan; Leding, Albin; Wilcox, Scott; Andersson Rasmussen, Anna; Leszczak, Kinga; Turunen, Lotta; Herrebout, Wouter; Hubert, Madlen; Bayer, Annette; Erdelyi, Mate. "NMR Backbone Assignment of VIM-2 and Identification of the Active Enantiomer of a Potential Inhibitor" ACS Med. Chem. Lett. 13, 257-261 (2022).

Assembly members:
entity_1, polymer, 240 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 Da.

Natural source: Common Name: Pseudomonas aeruginosa Taxonomy ID: 287 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas aeruginosa

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pDEST14

Entity Sequences (FASTA):
entity_1: VDSSGEYPTVSEIPVGEVRL YQIADGVWSHIATQSFDGAV YPSNGLIVRDGDELLLIDTA WGAKNTAALLAEIEKQIGLP VTRAVSTHFHDDRVGGVDVL RAAGVATYASPSTRRLAEVE GNEIPTHSLEGLSSSGDAVR FGPVELFYPGAAHSTDNLVV YVPSASVLYGGCAIYELSRT SAGNVADADLAEWPTSIERI QQHYPEAQFVIPGHGLPGGL DLLKHTTNVVKAHTNRSVVE

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	1438
15N chemical shifts	552
1H chemical shifts	552

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VIM-2	1
2	Zn, 1	2
3	Zn, 2	2

Entities:

Entity 1, VIM-2 240 residues - Formula weight is not available

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

Entity 2, Zn, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: VIM-2, [U-100% 13C; U-100% 15N], 500 uM; Zn 100 uM

sample_2: VIM-2, [U-100% 13C; U-100% 15N], 500 uM; Zn 100 uM; EtOH uM

sample_3: VIM2_EtOH_L-captopril, [U-100% 13C; U-100% 15N], 500 uM; Zn 100 uM; EtOH uM; L-captopril 750 uM

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 310 K

sample_conditions_2: pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D HNCO	sample_2	isotropic	sample_conditions_2
3D HN(CA)CO	sample_2	isotropic	sample_conditions_2
3D HNCA	sample_2	isotropic	sample_conditions_2
3D HNCACB	sample_2	isotropic	sample_conditions_2
3D HN(CO)CACB	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
3D HNCO	sample_3	isotropic	sample_conditions_2
3D HN(CA)CO	sample_3	isotropic	sample_conditions_2
3D HNCA	sample_3	isotropic	sample_conditions_2
3D HNCACB	sample_3	isotropic	sample_conditions_2
3D HN(CO)CACB	sample_3	isotropic	sample_conditions_2

Software:

CcpNMR - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 700 MHz
Bruker AVANCE NEO 600 MHz

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

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

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

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