BMRB Entry 18911
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PDB ID:
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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Title: NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TRANSPEPTIDASE ACYLATED BY ERTAPENEM PubMed: 23574509
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: 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).
Assembly members:
ERFK-YBIS-YCFS-YNHG, polymer, 129 residues, 14549.0884 Da.
entity_1RG, non-polymer, 477.531 Da.
Natural source: Common Name: Enterococcus faecium Taxonomy ID: 1352 Superkingdom: Bacteria Kingdom: not available Genus/species: Enterococcus faecium
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
ERFK-YBIS-YCFS-YNHG: GHMEDTYIEVDLENQHMWYY
KDGKVALETDIVSGKPTTPT
PAGVFYVWNKEEDATLKGTN
DDGTPYESPVNYWMPIDWTG
VGIHDSDWQPEYGGDLWKTR
GSHGCINTPPSVMKELFGMV
EKGTPVLVF
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 555 |
| 15N chemical shifts | 130 |
| 1H chemical shifts | 871 |
Additional metadata:
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 | TYR | ||||
| 3 | LYS | ASP | GLY | LYS | VAL | ALA | LEU | GLU | THR | ASP | ||||
| 4 | ILE | VAL | SER | GLY | LYS | PRO | THR | THR | PRO | THR | ||||
| 5 | PRO | ALA | GLY | VAL | PHE | TYR | VAL | TRP | ASN | LYS | ||||
| 6 | GLU | GLU | ASP | ALA | THR | LEU | LYS | GLY | THR | ASN | ||||
| 7 | ASP | 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 | GLY | ASP | LEU | TRP | LYS | THR | ARG | ||||
| 11 | GLY | SER | HIS | GLY | CYS | ILE | ASN | THR | PRO | 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
Related Database Links:
| UNP | Q3Y185_ENTFC |
| BMRB | 18900 |
| PDB | |
| GB | AFC64689 AFK60179 AGE31159 AGS76645 AII39985 |
| REF | WP_002287397 WP_002290929 WP_002296050 WP_002298179 WP_002307701 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts