BMRB Entry 18911

Name: NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TRANSPEPTIDASE ACYLATED BY ERTAPENEM
Published: 2013-04-22

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PDB ID: 3zgp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18911
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2012-12-19

Original release date:

2013-04-22

Authors:

Lecoq, L.; Triboulet, S.; Dubee, V.; Bougault, C.; Hugonnet, J.; Arthur, M.; Simorre, Jean-Pierre; Simorre, M.

Citation:

Citation: Lecoq, Lauriane; Dubee, Vincent; Triboulet, Sebastien; Bougault, Catherine; Hugonnet, Jean-Emmanuel; Arthur, Michel; Simorre, Jean-Pierre. "Structure of Enterococcus faeciuml,d-transpeptidase acylated by ertapenem provides insight into the inactivation mechanism." ACS Chem. Biol. 8, 1140-1146 (2013).
PubMed: 23574509

Assembly members:

Assembly members:
ERFK-YBIS-YCFS-YNHG, polymer, 129 residues, 14549.0884 Da.
entity_1RG, non-polymer, 477.531 Da.

Natural source:

Natural source: Common Name: Enterococcus faecium Taxonomy ID: 1352 Superkingdom: Bacteria Kingdom: not available Genus/species: Enterococcus faecium

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ERFK-YBIS-YCFS-YNHG: GHMEDTYIEVDLENQHMWYY KDGKVALETDIVSGKPTTPT PAGVFYVWNKEEDATLKGTN DDGTPYESPVNYWMPIDWTG VGIHDSDWQPEYGGDLWKTR GSHGCINTPPSVMKELFGMV EKGTPVLVF

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	555
15N chemical shifts	130
1H chemical shifts	871

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ERFK-YBIS-YCFS-YNHG	1
2	ligand 1RG	2

Entities:

Entity 1, ERFK-YBIS-YCFS-YNHG 129 residues - 14549.0884 Da.

1

GLY

HIS

MET

GLU

ASP

THR

TYR

ILE

GLU

VAL

2

ASP

LEU

GLU

ASN

GLN

HIS

MET

TRP

TYR

3

LYS

ASP

GLY

LYS

VAL

ALA

LEU

GLU

THR

ASP

4

ILE

VAL

SER

GLY

LYS

PRO

THR

PRO

THR

5

PRO

ALA

GLY

VAL

PHE

TYR

VAL

TRP

ASN

LYS

6

GLU

ASP

ALA

THR

LEU

LYS

GLY

THR

ASN

7

ASP

GLY

THR

PRO

TYR

GLU

SER

PRO

VAL

8

ASN

TYR

TRP

MET

PRO

ILE

ASP

TRP

THR

GLY

9

VAL

GLY

ILE

HIS

ASP

SER

ASP

TRP

GLN

PRO

10

GLU

TYR

GLY

ASP

LEU

TRP

LYS

THR

ARG

11

GLY

SER

HIS

GLY

CYS

ILE

ASN

THR

PRO

12

SER

VAL

MET

LYS

GLU

LEU

PHE

GLY

MET

VAL

13

GLU

LYS

GLY

THR

PRO

VAL

LEU

VAL

PHE

Entity 2, ligand 1RG - C22 H27 N3 O7 S - 477.531 Da.

1

1RG

Samples:

sample_1: ERFK-YBIS-YCFS-YNHG, [U-13C; U-15N], 0.9 mM; NaCl 300 mM

sample_2: ERFK-YBIS-YCFS-YNHG, [U-13C; U-15N], 0.9 mM; NaCl 300 mM

sample_conditions_1: ionic strength: 300.000 mM; pH: 6.400; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-15N-HSQC	sample_1	solution	sample_conditions_1
1H-13C-HSQC centered on aliphatics	sample_1	solution	sample_conditions_1
1H-15N-HMQC detecting 2J	sample_1	solution	sample_conditions_1
3J couplings in histidines imidazole ring	sample_1	solution	sample_conditions_1
HSQC detecting 1J coupling in histidines imidazole ring	sample_1	solution	sample_conditions_1
HNCACB	sample_1	solution	sample_conditions_1
HNCO	sample_1	solution	sample_conditions_1
3D-15N-NOESY-HSQC	sample_1	solution	sample_conditions_1
3D-13C-NOESY-HSQC centered on aliphatics	sample_1	solution	sample_conditions_1
1H-13C-HSQC centered on aromatics	sample_2	solution	sample_conditions_1
3D-13C-NOESY-HSQC centered on aromatics	sample_2	solution	sample_conditions_1
13C-15N-filtered NOESY	sample_2	solution	sample_conditions_1

Software:

CNS1.2 vany, BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN - chemical shift assignment

ANALYSIS vany, CCPN - chemical shift assignment

TALOS vany, Cornilescu, Delaglio and Bax - data analysis

UNIO v10, UNIO - data analysis

NMR spectrometers:

Varian Direct Drive 600 MHz
Varian Direct Drive 800 MHz
Bruker Avance 950 MHz

UNP	Q3Y185_ENTFC
BMRB	18900
PDB	1ZAT 2HKL 3ZG4 3ZGP
GB	AFC64689 AFK60179 AGE31159 AGS76645 AII39985
REF	WP_002287397 WP_002290929 WP_002296050 WP_002298179 WP_002307701
AlphaFold	Q3Y185