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BMRB: 18911

3ZGP

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

Authors

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

Assembly

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

Entity

1. ERFK-YBIS-YCFS-YNHG (polymer, Thiol state: all free), 129 monomers, 14559.03 Da Detail

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

2. NMR structure of the catalytic domain from E. faecium L,D-transpeptidase acylated by ertapenem, entity 1RG (non-polymer), 477.531 Da

Total weight

15036.562 Da

Max. entity weight

14559.03 Da

Source organism

Enterococcus faecium

Exptl. method

solution NMR

Refine. method

ARIA2.3

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 95.0 %, Completeness (bb): 92.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.0 % (1412 of 1487)	95.2 % (729 of 766)	94.9 % (559 of 589)	93.9 % (124 of 132)
Backbone	92.8 % (700 of 754)	92.0 % (241 of 262)	93.0 % (347 of 373)	94.1 % (112 of 119)
Sidechain	97.5 % (827 of 848)	96.8 % (488 of 504)	98.8 % (327 of 331)	92.3 % (12 of 13)
Aromatic	96.0 % (167 of 174)	96.6 % (84 of 87)	96.3 % (78 of 81)	83.3 % (5 of 6)
Methyl	99.2 % (117 of 118)	98.3 % (58 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 - ertapenem 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 - ertapenem 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

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.29 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.29 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.57 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-04-21

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: 18900 released on 2013-05-27
Title NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TRANSPEPTIDASE

Related entities 1. ERFK-YBIS-YCFS-YNHG, : 1 : 1 : 68 entities Detail

Experiments performed 12 experiments Detail

1 1H-15N-HSQC