BMRB Entry 19826

Name: Solution structure of sortase A from S. aureus in complex with benzo[d]isothiazol-3-one based inhibitor
Published: 2014-11-17

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PDB ID: 2mlm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19826
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of sortase A from S. aureus in complex with benzo[d]isothiazol-3-one based inhibitor

Deposition date:

2014-03-03

Original release date:

2014-11-17

Authors:

Jaudzems, Kristaps; Zhulenkovs, Dmitry; Leonchiks, Ainars

Citation:

Citation: Jaudzems, Kristaps; Zhulenkovs, Dmitry; Leonchiks, Ainars. "Solution structure of sortase A from S. aureus in complex with benzo[d]isothiazol-3-one based inhibitor" Bioorg. Med. Chem. ., .-. (2014).
PubMed: 25282649

Assembly members:

Assembly members:
sortase_A, polymer, 148 residues, 16807.176 Da.
entity_2W7, non-polymer, 344.471 Da.

Natural source:

Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET23a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
sortase_A: MQAKPQIPKDKSKVAGYIEI PDADIKEPVYPGPATPEQLN RGVSFAEENESLDDQNISIA GHTFIDRPNYQFTNLKAAKK GSMVYFKVGNETRKYKMTSI RDVKPTDVEVLDEQKGKDKQ LTLITCDDYNEKTGVWEKRK IFVATEVK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	660
15N chemical shifts	148
1H chemical shifts	1035

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	sortase_A	1
2	inhibitor_2W7	2

Entities:

Entity 1, sortase_A 148 residues - 16807.176 Da.

Residue 126 (UNK) is a covalently modified cysteine

1

MET

GLN

ALA

LYS

PRO

GLN

ILE

PRO

LYS

ASP

2

LYS

SER

LYS

VAL

ALA

GLY

TYR

ILE

GLU

ILE

3

PRO

ASP

ALA

ASP

ILE

LYS

GLU

PRO

VAL

TYR

4

PRO

GLY

PRO

ALA

THR

PRO

GLU

GLN

LEU

ASN

5

ARG

GLY

VAL

SER

PHE

ALA

GLU

ASN

GLU

6

SER

LEU

ASP

GLN

ASN

ILE

SER

ILE

ALA

7

GLY

HIS

THR

PHE

ILE

ASP

ARG

PRO

ASN

TYR

8

GLN

PHE

THR

ASN

LEU

LYS

ALA

LYS

9

GLY

SER

MET

VAL

TYR

PHE

LYS

VAL

GLY

ASN

10

GLU

THR

ARG

LYS

TYR

LYS

MET

THR

SER

ILE

11

ARG

ASP

VAL

LYS

PRO

THR

ASP

VAL

GLU

VAL

12

LEU

ASP

GLU

GLN

LYS

GLY

LYS

ASP

LYS

GLN

13

LEU

THR

LEU

ILE

THR

CYS

ASP

TYR

ASN

14

GLU

LYS

THR

GLY

VAL

TRP

GLU

LYS

ARG

LYS

15

ILE

PHE

VAL

ALA

THR

GLU

VAL

LYS

Entity 2, inhibitor_2W7 - C19 H24 N2 O2 S - 344.471 Da.

1

2W7

Samples:

sample_1: sortase A, [U-100% 13C; U-100% 15N], 1.6 ± 0.2 mM; N-(adamantan-1-yl)-2-(3-oxo-2,3-dihydro-1,2-benzothiazol-2-yl)-acetamide 2.4 ± 0.2 mM; D2O, [U-100% 2H], 5.0 ± 0.5 %; DMSO, [U-100% 2H], 2.4 ± 0.2 %; sodium acetate, [U-100% 2H], 20 ± 2 mM; sodium chloride 50 ± 5 mM; calcium chloride 10 ± 2 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D (F1)-15N,13C-filtered 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D (F1,F2)-13C,15N-filtered NOESY	sample_1	isotropic	sample_conditions_1
2D (F1,F2)-13C,15N-filtered TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution

TOPSPIN v3.2, Bruker Biospin - processing

VNMRJ v2.1b, Varian - collection

CARA v1.9.0, R. Keller - chemical shift assignment

UNIO v2.0.2, T. Herrmann, F. Fiorito, J. Volk - data analysis, peak picking, structure solution

NMR spectrometers:

Varian INOVA 600 MHz

BMRB	16270 19624
PDB	1IJA 1T2O 1T2P 1T2W 2KID 2MLM
DBJ	BAB43619 BAB58690 BAB96313 BAF68698 BAF79395
EMBL	CAG41587 CAG44229 CAI82090 CAQ50958 CBI50513
GB	AAD48437 AAW37316 ABD22861 ABD31836 ABQ50328
REF	WP_000759357 WP_000759358 WP_000759359 WP_000759360 WP_000759361