BMRB Entry 19422

Name: Structural Basis of a Thiopeptide Antibiotic Multidrug Resistance System from Streptomyces lividans:Nosiheptide in Complex with TipAS
Published: 2014-12-08

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PDB ID: 2mc0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19422
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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:

Structural Basis of a Thiopeptide Antibiotic Multidrug Resistance System from Streptomyces lividans:Nosiheptide in Complex with TipAS

Deposition date:

2013-08-12

Original release date:

2014-12-08

Authors:

Habazettl, Judith; Allan, Martin; Jensen, Pernille; Sass, Hans-Juergen; Grzesiek, Stephan

Citation:

Citation: Habazettl, Judith; Allan, Martin; Jensen, Pernille; Sass, J rgen; Grzesiek, Stephan. "Structural Basis of a Thiopeptide Antibiotic Multidrug Resistance System from Streptomyces lividans" .

Assembly members:

Assembly members:
TipAS, polymer, 144 residues, 16453.025 Da.
nosiheptide, polymer, 14 residues, 1050.172 Da.

Natural source:

Natural source: Common Name: Streptomyces lividans Taxonomy ID: 1916 Superkingdom: Bacteria Kingdom: not available Genus/species: Streptomyces lividans

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pDS8

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TipAS: MGINLTPEEKFEVFGDFDPD QYEEEVRERWGNTDAYRQSK EKTASYTKEDWQRIQDEADE LTRRFVALMDAGEPADSEGA MDAAEDHRQGIARNHYDCGY EMHTCLGEMYVSDERFTRNI DAAKPGLAAYMRDAILANAV RHTP
nosiheptide: SXTXXXXCXXXXXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	600
15N chemical shifts	153
1H chemical shifts	983

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TipAS	1
2	nosiheptide	2

Entities:

Entity 1, TipAS 144 residues - 16453.025 Da.

TipAS is the short isoform of TipA. It is the C terminal domain from residue M110 to P253.

1

MET

GLY

ILE

ASN

LEU

THR

PRO

GLU

LYS

2

PHE

GLU

VAL

PHE

GLY

ASP

PHE

ASP

PRO

ASP

3

GLN

TYR

GLU

VAL

ARG

GLU

ARG

TRP

4

GLY

ASN

THR

ASP

ALA

TYR

ARG

GLN

SER

LYS

5

GLU

LYS

THR

ALA

SER

TYR

THR

LYS

GLU

ASP

6

TRP

GLN

ARG

ILE

GLN

ASP

GLU

ALA

ASP

GLU

7

LEU

THR

ARG

PHE

VAL

ALA

LEU

MET

ASP

8

ALA

GLY

GLU

PRO

ALA

ASP

SER

GLU

GLY

ALA

9

MET

ASP

ALA

GLU

ASP

HIS

ARG

GLN

GLY

10

ILE

ALA

ARG

ASN

HIS

TYR

ASP

CYS

GLY

TYR

11

GLU

MET

HIS

THR

CYS

LEU

GLY

GLU

MET

TYR

12

VAL

SER

ASP

GLU

ARG

PHE

THR

ARG

ASN

ILE

13

ASP

ALA

LYS

PRO

GLY

LEU

ALA

TYR

14

MET

ARG

ASP

ALA

ILE

LEU

ALA

ASN

ALA

VAL

15

ARG

HIS

THR

PRO

Entity 2, nosiheptide 14 residues - 1050.172 Da.

1

SER

BB9

THR

DBU

BB9

3GL

BB9

CYS

BB9

MH6

2

BB9

DHA

NH2

NO1

Samples:

sample_1: TipAS, [U-98% 15N], 1 mM; nosiheptide 2 mM; potassium phosphate 50 mM; sodium azide 0.02 w/v; H2O 95%; D2O 5%

sample_2: TipAS, [U-99% 13C; U-99% 15N], 1 mM; nosiheptide 2 mM; potassium phosphate 50 mM; sodium azide 0.02 w/v; H2O 95%; D2O 5%

sample_3: TipAS, [U-99% 13C; U-99% 15N], 1 mM; nosiheptide 2 mM; potassium phosphate 50 mM; sodium azide 0.02 w/v; D2O 100%

sample_4: TipAS, [U-99% 13C; U-99% 15N], 0.8 mM; nosiheptide 1.6 mM; potassium phosphate 10 mM; Pf1 phage 10 mg/mL; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.055 M; pH: 5.9; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.055 M; pH: 5.9; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 0.055 M; pD: 5.9; pressure: 1 atm; temperature: 298 K

sample_conditions_4: ionic strength: 0.011 M; pH: 5.9; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_3
3D HNCO	sample_2	isotropic	sample_conditions_2
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_2
3D C(CO)NH	sample_2	isotropic	sample_conditions_2
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_2
3D HC(CO)NH TOCSY	sample_2	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_3
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_3
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_3
2D 1H-1H NOESY/filter against 13C-15N	sample_3	isotropic	sample_conditions_3
2D 1H-1H NOESY/filter against 13C-15N	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY/filter against 13C-15N	sample_3	isotropic	sample_conditions_3
Doublet-separated 2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
Doublet-separated 2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_4
J-resolved ct 13C-HSQC	sample_2	isotropic	sample_conditions_2
J-resolved ct 13C-HSQC	sample_4	isotropic	sample_conditions_4
3D CBCANH	sample_2	isotropic	sample_conditions_2

Software:

X-PLOR NIH v2.30, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRPipe v2012, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.115, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - experiment/data collection

PIPP, Garrett - peak picking

XEASY, Bartels et al. - chemical shift assignment

TALOS vTALOS+, Cornilescu, Delaglio and Bax - dihedral angle prediction

ProcheckNMR, Laskowski and MacArthur - structure analysis

xwinnmr, Bruker Biospin - experiment/data collection

NMR spectrometers:

Bruker DRX 600 MHz
Bruker DRX 800 MHz

BMRB	19421
PDB	1NY9 2MBZ 2MC0
DBJ	BAD11210 BAD11216 BAD11222 BAD11228 BAD11234
EMBL	CAB42766
GB	AAB27737 AAC13653 AIJ15084 AIV35032 EFD68501
REF	NP_627619 WP_003975420 WP_007452041 WP_052836374
SP	P0A4T8 P0A4T9
AlphaFold	P0A4T8 P0A4T9