BMRB Entry 18037
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18037
MolProbity Validation Chart
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Title: NMR STRUCTURE OF THE IMIPENEM-ACYLATED L,D-TRANSPEPTIDASE FROM BACILLUS SUBTILIS PubMed: 22579252
Deposition date: 2011-11-01 Original release date: 2012-05-22
Authors: Lecoq, Lauriane; Simorre, Jean-Pierre; Bougault, Catherine; Arthur, Michel; Hugonnet, Jean-Emmanuel; Veckerle, Carole; Pessey, Ombeline
Citation: Lecoq, Lauriane; Bougault, Catherine; Hugonnet, Jean-Emmanuel; Veckerle, Carole; Pessey, Ombeline; Arthur, Michel; Simorre, Jean-Pierre. "Dynamics Induced by beta-Lactam Antibiotics in the Active Site of Bacillus subtilisl,d-Transpeptidase." Structure 20, 850-861 (2012).
Assembly members:
ykud_imip, polymer, 175 residues, 18954.8503 Da.
Natural source: Common Name: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 Taxonomy ID: 224308 Superkingdom: not available Kingdom: Bacteria Genus/species: not available Bacillus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
ykud_imip: GRKLLTYQVKQGDTLNSIAA
DFRISTAALLQANPSLQAGL
TAGQSIVIPGLPDPYTIPYH
IAVSIGAKTLTLSLNNRVMK
TYPIAVGKILTQTPTGEFYI
INRQRNPGGPFGAYWLSLSK
QHYGIHGTNNPASIGKAVSK
GCIRMHNKDVIELASIVPNG
TRVTINRGSHHHHHH
- assigned_chemical_shifts
- RDCs
- assigned_chemical_shifts
- heteronucl_NOEs
- heteronucl_T1_relaxation
- heteronucl_T2_relaxation
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 643 |
| 15N chemical shifts | 164 |
| 1H chemical shifts | 1044 |
| T1 relaxation values | 116 |
| T2 relaxation values | 114 |
| heteronuclear NOE values | 117 |
| residual dipolar couplings | 191 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ykud imip | 1 |
Entities:
Entity 1, ykud imip 175 residues - 18954.8503 Da.
| 1 | GLY | ARG | LYS | LEU | LEU | THR | TYR | GLN | VAL | LYS | ||||
| 2 | GLN | GLY | ASP | THR | LEU | ASN | SER | ILE | ALA | ALA | ||||
| 3 | ASP | PHE | ARG | ILE | SER | THR | ALA | ALA | LEU | LEU | ||||
| 4 | GLN | ALA | ASN | PRO | SER | LEU | GLN | ALA | GLY | LEU | ||||
| 5 | THR | ALA | GLY | GLN | SER | ILE | VAL | ILE | PRO | GLY | ||||
| 6 | LEU | PRO | ASP | PRO | TYR | THR | ILE | PRO | TYR | HIS | ||||
| 7 | ILE | ALA | VAL | SER | ILE | GLY | ALA | LYS | THR | LEU | ||||
| 8 | THR | LEU | SER | LEU | ASN | ASN | ARG | VAL | MET | LYS | ||||
| 9 | THR | TYR | PRO | ILE | ALA | VAL | GLY | LYS | ILE | LEU | ||||
| 10 | THR | GLN | THR | PRO | THR | GLY | GLU | PHE | TYR | ILE | ||||
| 11 | ILE | ASN | ARG | GLN | ARG | ASN | PRO | GLY | GLY | PRO | ||||
| 12 | PHE | GLY | ALA | TYR | TRP | LEU | SER | LEU | SER | LYS | ||||
| 13 | GLN | HIS | TYR | GLY | ILE | HIS | GLY | THR | ASN | ASN | ||||
| 14 | PRO | ALA | SER | ILE | GLY | LYS | ALA | VAL | SER | LYS | ||||
| 15 | GLY | CYS | ILE | ARG | MET | HIS | ASN | LYS | ASP | VAL | ||||
| 16 | ILE | GLU | LEU | ALA | SER | ILE | VAL | PRO | ASN | GLY | ||||
| 17 | THR | ARG | VAL | THR | ILE | ASN | ARG | GLY | SER | HIS | ||||
| 18 | HIS | HIS | HIS | HIS | HIS |
Samples:
YkuD_imip_MES: ykud_imipenem2.5eq, [U-100% 13C; U-100% 15N], 0.7 mM; MES 12.5 mM; NaCl 150 mM; H2O 90%; D2O 10%
condition1: ionic strength: 0.150 M; pH: 6.500; pressure: 1.000 atm; temperature: 298.000 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H-13C NOESY | YkuD_imip_MES | isotropic | condition1 |
| 2D 1H-13C HSQC/HMQC | YkuD_imip_MES | isotropic | condition1 |
| Expt_46 (h[C]_H[C].NOESY) | YkuD_imip_MES | isotropic | condition1 |
| 3D 1H-15N NOESY | YkuD_imip_MES | isotropic | condition1 |
| 3D HNCO | YkuD_imip_MES | isotropic | condition1 |
| 3D HNCACB | YkuD_imip_MES | isotropic | condition1 |
| 2D 1H-15N HSQC/HMQC | YkuD_imip_MES | isotropic | condition1 |
| 2D 1H-13C HSQC/HMQC | YkuD_imip_MES | isotropic | condition1 |
| 2D 1H-15N HSQC/HMQC | YkuD_imip_MES | isotropic | condition1 |
| 3D 1H-13C NOESY | YkuD_imip_MES | isotropic | condition1 |
Software:
CNS v1.2, Brunger - Structure calculation
CcpNmr_Analysis v2.1, CCPN - Spectrum analysis and assignment
TALOS vany, TALOS - Prediction of torsion angles
UNIO v10, UNIO - Automated peakpicking and NOE assignment
nmrDraw vany, NMRPipe - Spectrum display
nmrPipe vany, NMRPipe - Spectrum processing
ARIA v2.3, ARIA - Structure calculation
NMR spectrometers:
- Bruker Avance 900 MHz
- Varian Direct Drive 800 MHz
- Varian Direct Drive 600 MHz
- Bruker Avance 800 MHz
Related Database Links:
| UNP | YKUD_BACSU |
| BMRB | 17701 25192 |
| PDB | |
| DBJ | BAI85015 BAM52048 BAM57625 GAK78521 |
| EMBL | CAA10867 CAB13277 CCU57969 CEI56583 CEJ76989 |
| GB | ADV96423 AEP90550 AFQ57337 AGA22168 AGE63257 |
| REF | NP_389287 WP_009968919 WP_010886500 WP_014479657 WP_015252194 |
| SP | O34816 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts