BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 17701

Title: 20 NMR solution structures of Bacillus subtilis L,D-transpeptidase refined in water   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 subtilis L,D-Transpeptidase"  Structure 20, 850-861 (2012).

Assembly members:
ykud_no_mutations, polymer, 175 residues, Formula weight is not available

Natural source:   Common Name: BACILLUS SUBTILIS SUBSP. SUBTILIS   Taxonomy ID: 135461   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Bacillus subtilis

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

Entity Sequences (FASTA):
ykud_no_mutations: GRKLLTYQVKQGDTLNSIAA DFRISTAALLQANPSLQAGL TAGQSIVIPGLPDPYTIPYH IAVSIGAKTLTLSLNNRVMK TYPIAVGKILTQTPTGEFYI INRQRNPGGPFGAYWLSLSK QHYGIHGTNNPASIGKAVSK GCIRMHNKDVIELASIVPNG TRVTINRGSHHHHHH

Data typeCount
13C chemical shifts732
15N chemical shifts187
1H chemical shifts1171

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ykud_no_mutations1

Entities:

Entity 1, ykud_no_mutations 175 residues - Formula weight is not available

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:

sample_1: ykud_no_mutations, [U-100% 13C; U-100% 15N], 0.7 mM; MES 12.5 mM; NaCl 150 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.150 M; pH: 6.500; pressure: 1 atm; temperature: 298.000 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC/HMQCsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
2D 1H-13C HSQC/HMQCsample_1isotropicsample_conditions_1
Expt_52 (h[C]_H[C].NOESY)sample_1isotropicsample_conditions_1
2D 1H-13C HSQC/HMQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQC/HMQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1

Software:

CNS_1.2, Brunger, Adams, Clore, Gros, Nilges and Read - Structure calculation

CcpNmr_Analysis_2.1, CCPN - Spectrum analysis and assignment

TALOS, Cornilescu, Delaglio and Bax - Prediction of torsion angles

UNIO, UNIO - Automated peakpicking and NOE assignment

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - Spectrum display

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - Spectrum processing

ARIA_2.3, Linge, O'Donoghue and Nilges - Structure calculation

NMR spectrometers:

  • Varian vnmrs 800 MHz
  • Bruker Avance 900 MHz
  • Varian vnmrs 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 18037 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