BMRB Entry 18037

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

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).
PubMed: 22579252

Assembly members:

Assembly members:
ykud_imip, polymer, 175 residues, 18954.8503 Da.

Natural source:

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:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET2818

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
AlphaFold Q796K7 O34816

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks