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BMRB: 26952

5A5Z

92% Backbone 1H, 13C, and 15N Chemical Shift Assignments for New Delhi beta lactamase 1 (without Zinc)

Authors

Riviere, G., Morellet, N.

Assembly

NDM-1 (without ligand , without Zn)

Entity

1. NDM-1 (without ligand , without Zn) (polymer, Thiol state: unknown), 253 monomers, 27076.14 Da Detail

MGEIRPTIGQ QMETGDQRFG DLVFRQLAPN VWQHTSYLDM PGFGAVASNG LIVRDGGRVL VVDTAWTDDQ TAQILNWIKQ EINLPVALAV VTHAHQDKMG GMDALHAAGI ATYANALSNQ LAPQEGMVAA QHSLTFAANG WVEPATAPNF GPLKVFYPGP GHTSDNITVG IDGTDIAFGG CLIKDSKAKS LGNLGDADTE HYAASARAFG AAFPKASMIV MSHSAPDSRA AITHTARMAD KLRLEHHHHH HHH

Formula weight

27076.14 Da

Source organism

Escherichia coli

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 38.5 %, Completeness (bb): 71.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	38.5 % (1073 of 2785)	16.1 % (228 of 1417)	57.2 % (625 of 1092)	79.7 % (220 of 276)
Backbone	71.9 % (1074 of 1494)	44.0 % (228 of 518)	85.0 % (625 of 735)	91.7 % (221 of 241)
Sidechain	11.4 % (173 of 1520)	0.0 % (0 of 899)	29.5 % (173 of 586)	0.0 % (0 of 35)
Aromatic	0.0 % (0 of 238)	0.0 % (0 of 119)	0.0 % (0 of 115)	0.0 % (0 of 4)
Methyl	11.8 % (34 of 288)	0.0 % (0 of 144)	23.6 % (34 of 144)

1. New Delhi Beta Lactamase 1

MGEIRPTIGQ QMETGDQRFG DLVFRQLAPN VWQHTSYLDM PGFGAVASNG LIVRDGGRVL VVDTAWTDDQ TAQILNWIKQ EINLPVALAV VTHAHQDKMG GMDALHAAGI ATYANALSNQ LAPQEGMVAA QHSLTFAANG WVEPATAPNF GPLKVFYPGP GHTSDNITVG IDGTDIAFGG CLIKDSKAKS LGNLGDADTE HYAASARAFG AAFPKASMIV MSHSAPDSRA AITHTARMAD KLRLEHHHHH HHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

Release date

2016-11-21

Citation

NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors
Riviere, G., Oueslati, S., Gayral, M., Crechet, J.B., Nhiri, N., Jacquet, E., Cintrat, J.C., Giraud, F., van Heijenoort, C., Lescop, E., Pethe, S., Iorga, B.I., Naas, T., Guittet, E., Morellet, N.
ACS Omega (2020), 5, 10466-10480, PubMed 32426604 , DOI 10.1021/acsomega.0c00590 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26950 released on 2016-11-21
Title Backbone 1H, 13C, and 15N Chemical Shift Assignments for New Delhi beta lactamase 1 (in presence of Zn ions).

Related entities 1. NDM-1 (without ligand , without Zn), : 1 : 91 : 22 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

2 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

5 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

6 3D HN(COCA)CB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

7 3D HCACO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 50mM phosphate sodium pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	New Delhi Beta Lactamase 1	[U-100% 13C; U-100% 15N; U-80% 2H]		0.75 mM
2	phosphate sodium	natural abundance		50 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr26952_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr26952_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1057		93.3 (chain: 1, length: 253)
1	Chemical shift references	chemical_shift_reference_1	Warning	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 253, Sequence coverage: 93.3%
- Total number of assignments
  - ¹³C chemical shifts: 619
  - ¹H chemical shifts: 219
  - ¹⁵N chemical shifts: 219
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords Molecular modeling, NDM-1, Nuclear magnetic resonance, flavonoids, zinc