BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18037

Title: NMR STRUCTURE OF THE IMIPENEM-ACYLATED L,D-TRANSPEPTIDASE FROM BACILLUS SUBTILIS   PubMed: 22579252

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

Data typeCount
13C chemical shifts643
15N chemical shifts164
1H chemical shifts1044
T1 relaxation values116
T2 relaxation values114
heteronuclear NOE values117
residual dipolar couplings191

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1ykud imip1

Entities:

Entity 1, ykud imip 175 residues - 18954.8503 Da.

1   GLYARGLYSLEULEUTHRTYRGLNVALLYS
2   GLNGLYASPTHRLEUASNSERILEALAALA
3   ASPPHEARGILESERTHRALAALALEULEU
4   GLNALAASNPROSERLEUGLNALAGLYLEU
5   THRALAGLYGLNSERILEVALILEPROGLY
6   LEUPROASPPROTYRTHRILEPROTYRHIS
7   ILEALAVALSERILEGLYALALYSTHRLEU
8   THRLEUSERLEUASNASNARGVALMETLYS
9   THRTYRPROILEALAVALGLYLYSILELEU
10   THRGLNTHRPROTHRGLYGLUPHETYRILE
11   ILEASNARGGLNARGASNPROGLYGLYPRO
12   PHEGLYALATYRTRPLEUSERLEUSERLYS
13   GLNHISTYRGLYILEHISGLYTHRASNASN
14   PROALASERILEGLYLYSALAVALSERLYS
15   GLYCYSILEARGMETHISASNLYSASPVAL
16   ILEGLULEUALASERILEVALPROASNGLY
17   THRARGVALTHRILEASNARGGLYSERHIS
18   HISHISHISHISHIS

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:

NameSampleSample stateSample conditions
3D 1H-13C NOESYYkuD_imip_MESisotropiccondition1
2D 1H-13C HSQC/HMQCYkuD_imip_MESisotropiccondition1
Expt_46 (h[C]_H[C].NOESY)YkuD_imip_MESisotropiccondition1
3D 1H-15N NOESYYkuD_imip_MESisotropiccondition1
3D HNCOYkuD_imip_MESisotropiccondition1
3D HNCACBYkuD_imip_MESisotropiccondition1
2D 1H-15N HSQC/HMQCYkuD_imip_MESisotropiccondition1
2D 1H-13C HSQC/HMQCYkuD_imip_MESisotropiccondition1
2D 1H-15N HSQC/HMQCYkuD_imip_MESisotropiccondition1
3D 1H-13C NOESYYkuD_imip_MESisotropiccondition1

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