BMRB Entry 18037

Name: NMR STRUCTURE OF THE IMIPENEM-ACYLATED L,D-TRANSPEPTIDASE FROM BACILLUS SUBTILIS
Published: 2012-05-22

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PDB ID: 4a52
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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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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

Entity Sequences (FASTA):

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

Data sets:

RDCs
- RDC_list_1
- RDC_list_2
assigned_chemical_shifts
- assigned_chem_shift_list
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
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
Samples and Experiments
Software
Spectrometers
Hide all

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

THR

TYR

GLN

VAL

LYS

2

GLN

GLY

ASP

THR

LEU

ASN

SER

ILE

ALA

3

ASP

PHE

ARG

ILE

SER

THR

ALA

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

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

PRO

12

PHE

GLY

ALA

TYR

TRP

LEU

SER

LEU

SER

LYS

13

GLN

HIS

TYR

GLY

ILE

HIS

GLY

THR

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

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

UNP	YKUD_BACSU
BMRB	17701 25192
PDB	1Y7M 2MTZ 3ZQD 4A1I 4A1J 4A1K 4A52
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