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BMRB: 18900

3ZG4

NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TRANSPEPTIDASE

Authors

Lecoq, L., Dubee, V., Triboulet, S., Bougault, C., Hugonnet, J.E., Arthur, M., Simorre, J., Simorre, M.

Assembly

NMR structure of the catalytic domain from E. faecium L,D-transpeptidase

Entity

1. NMR structure of the catalytic domain from E. faecium L,D-transpeptidase (polymer, Thiol state: all free), 129 monomers, 14559.03 Da Detail

GHMEDTYIEV DLENQHMWYY KDGKVALETD IVSGKPTTPT PAGVFYVWNK EEDATLKGTN DDGTPYESPV NYWMPIDWTG VGIHDSDWQP EYGGDLWKTR GSHGCINTPP SVMKELFGMV EKGTPVLVF

Formula weight

14559.03 Da

Source organism

Enterococcus faecium

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 97.1 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.1 % (1444 of 1487)	97.0 % (743 of 766)	97.3 % (573 of 589)	97.0 % (128 of 132)
Backbone	96.4 % (727 of 754)	95.4 % (250 of 262)	96.8 % (361 of 373)	97.5 % (116 of 119)
Sidechain	98.1 % (832 of 848)	97.8 % (493 of 504)	98.8 % (327 of 331)	92.3 % (12 of 13)
Aromatic	98.9 % (172 of 174)	100.0 % (87 of 87)	97.5 % (79 of 81)	100.0 % (6 of 6)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. ERFK-YBIS-YCFS-YNHG

GHMEDTYIEV DLENQHMWYY KDGKVALETD IVSGKPTTPT PAGVFYVWNK EEDATLKGTN DDGTPYESPV NYWMPIDWTG VGIHDSDWQP EYGGDLWKTR GSHGCINTPP SVMKELFGMV EKGTPVLVF

Show sample condition

Sample #1

Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

Sample #2

Solvent system 100% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
3	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
4	NaCl	natural abundance		300 mM

LACS Plot; CA

Referencing offset: 0.4 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.4 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.48 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 3ZG4, Strand ID: A Detail

Release date

2013-05-27

Citation

Structure of Enterococcus faeciuml,d-transpeptidase acylated by ertapenem provides insight into the inactivation mechanism
Lecoq, L., Dubee, V., Triboulet, S., Bougault, C., Hugonnet, J., Arthur, M., Simorre, J.
ACS Chem. Biol. (2013), 8, 1140-1146, PubMed 23574509 , DOI 10.1021/cb4001603 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18911 released on 2013-04-21
Title NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TRANSPEPTIDASE ACYLATED BY ERTAPENEM

Related entities 1. NMR structure of the catalytic domain from E. faecium L,D-transpeptidase, : 1 : 1 : 68 entities Detail

Experiments performed 10 experiments Detail

1 1H-15N-HSQC

Instrument

Varian Direct Drive - 800 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

2 1H-13C-HSQC centered on aliphatics

Instrument

Varian Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

3 1H-15N-HMQC detecting 2J

Instrument

Varian Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

4 3J couplings in histidines imidazole ring

Instrument

Varian Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

5 1H-15N-HSQC detecting 1J coupling in histidines imidazole ring

Instrument

Varian Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

6 3D-15N-NOESY-HSQC

Instrument

Varian Direct Drive - 800 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

7 HNCO

Instrument

Varian Direct Drive - 600 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

8 3D-13C-NOESY-HSQC centered on aliphatics

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
1	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
2	NaCl	natural abundance		300 mM

9 1H-13C-HSQC centered on aromatics

Instrument

Varian Direct Drive - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
3	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
4	NaCl	natural abundance		300 mM

10 3D-13C-NOESY-HSQC centered on aromatics

Instrument

Varian Direct Drive - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.400, Details Ldtfm 0.9 mM

#	Name	Isotope labeling	Type	Concentration
3	ERFK-YBIS-YCFS-YNHG	[U-13C; U-15N]		0.9 mM
4	NaCl	natural abundance		300 mM

nullKeywords antibiotic resistance, Ldtfm, peptidoglycan biosynthesis, TRANSFERASE, transpeptidation