BMRB Entry 34379

Name: Solution structure of sortase A from S. aureus in complex with 2-(aminomethyl)-3-hydroxy-4H-pyran-4-one based prodrug
Published: 2020-01-17

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PDB ID: 6r1v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34379
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
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 2-(aminomethyl)-3-hydroxy-4H-pyran-4-one based prodrug

Deposition date:

2019-03-15

Original release date:

2020-01-17

Authors:

Jaudzems, K.; Leonchiks, A.

Citation:

Citation: Jaudzems, Kristaps; Kurbatska, Viktorija; Je Kabsons, Atis; Bobrovs, Raitis; Rudevica, Zhanna; Leonchiks, Ainars. "Targeting Bacterial Sortase A with Covalent Inhibitors: 27 New Starting Points for Structure-Based Hit-to-Lead Optimization" ACS Infect. Dis. 6, 186-194 (2020).
PubMed: 31724850

Assembly members:

Assembly members:
entity_1, polymer, 148 residues, 16825.062 Da.
entity_JPT, non-polymer, 240.276 Da.

Natural source:

Natural source: Common Name: Staphylococcus aureus subsp. aureus NCTC 8325 Taxonomy ID: 93061 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MQAKPQIPKDKSKVAGYIEI PDADIKEPVYPGPATPEQLN RGVSFAEENESLDDQNISIA GHTFIDRPNYQFTNLKAAKK GSMVYFKVGNETRKYKMTSI RDVKPTDVEVLDEQKGKDKQ LTLITCDDYNEKTGVWEKRK IFVATEVK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	663
15N chemical shifts	149
1H chemical shifts	1055

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 148 residues - 16825.062 Da.

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, entity_2 - C11 H10 O4 S - 240.276 Da.

1

JPT

Samples:

sample_1: Sortase A protein, [U-13C; U-15N], 1.6 ± 0.2 mM; 3-hydroxy-6-(hydroxymethyl)-2-(thiophen-3-ylmethyl)-4H-pyran-4-one 3.2 ± 0.2 mM; sodium acetate 20 ± 2 mM; sodium chloride 50 ± 5 mM; calcium chloride 10 ± 1 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
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 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D (F1,F2)-13C,15N-filtered TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	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 - structure calculation

CYANA, Guntert, Mumenthaler and Wuthrich - data analysis

TOPSPIN, Bruker Biospin - processing

VNMR v2.1b, Varian - collection

CARA v1.9, Keller and Wuthrich - chemical shift assignment

UNIO, T. Herrmann, F. Fiorito, J. Volk - data analysis, peak picking

NMR spectrometers:

Varian INOVA 600 MHz

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