BMRB Entry 17784

Name: NMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1
Published: 2012-04-18

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PDB ID: 2lfw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17784
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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:

NMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1

Deposition date:

2011-07-18

Original release date:

2012-04-18

Authors:

Campagne, Sebastien; Damberger, Fred; Vorholt, Julia; Allain, Frederic

Citation:

Citation: Campagne, Sebastien; Damberger, Fred; Kaczmarczyk, Andreas; Francez-Charlot, Anne; Allain, Frederic H-T; Vorholt, Julia. "Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria." Proc. Natl. Acad. Sci. U.S.A. 109, E1405-E1414 (2012).
PubMed: 22550171

Assembly members:

Assembly members:
PhyR_sigma_like_domain, polymer, 157 residues, 17336.539 Da.
NepR_anti_sigma_factor, polymer, 62 residues, 6923.098 Da.

Natural source:

Natural source: Common Name: Sphingomonas sp. Fr1 Taxonomy ID: 907061 Superkingdom: Bacteria Kingdom: not available Genus/species: Sphingomonas Sphingomonas sp. Fr1

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET26bII-PhyRSL

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PhyR_sigma_like_domain: MSLGQQLAPHLPFLRRYGRA LTGSQNQGDKYVRATLEAIV AAPDQFPRDVDPRLGLYRMF QGIWASANADGEAQTSQSDA EGTEAVARARLARMTPLSRQ ALLLTAMEGFSPEDAAYLIE VDTSEVETLVTEALAEIEKQ TRALELVPRGSHHHHHH
NepR_anti_sigma_factor: MLDLPGNKDKKASSKKSPAK VQSKDRDMGAALRSAYQKTI EEQVPDEMLDLLNKLALELV PR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	831
15N chemical shifts	212
1H chemical shifts	1415

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PhyR_sigma_like_domain	1
2	NepR_anti_sigma_factor	2

Entities:

Entity 1, PhyR_sigma_like_domain 157 residues - 17336.539 Da.

From residue 144 to 157, amino acid residues of thrombin cleavage site + his tag

1

MET

SER

LEU

GLY

GLN

LEU

ALA

PRO

HIS

2

LEU

PRO

PHE

LEU

ARG

TYR

GLY

ARG

ALA

3

LEU

THR

GLY

SER

GLN

ASN

GLN

GLY

ASP

LYS

4

TYR

VAL

ARG

ALA

THR

LEU

GLU

ALA

ILE

VAL

5

ALA

PRO

ASP

GLN

PHE

PRO

ARG

ASP

VAL

6

ASP

PRO

ARG

LEU

GLY

LEU

TYR

ARG

MET

PHE

7

GLN

GLY

ILE

TRP

ALA

SER

ALA

ASN

ALA

ASP

8

GLY

GLU

ALA

GLN

THR

SER

GLN

SER

ASP

ALA

9

GLU

GLY

THR

GLU

ALA

VAL

ALA

ARG

ALA

ARG

10

LEU

ALA

ARG

MET

THR

PRO

LEU

SER

ARG

GLN

11

ALA

LEU

THR

ALA

MET

GLU

GLY

PHE

12

SER

PRO

GLU

ASP

ALA

TYR

LEU

ILE

GLU

13

VAL

ASP

THR

SER

GLU

VAL

GLU

THR

LEU

VAL

14

THR

GLU

ALA

LEU

ALA

GLU

ILE

GLU

LYS

GLN

15

THR

ARG

ALA

LEU

GLU

LEU

VAL

PRO

ARG

GLY

16

SER

HIS

Entity 2, NepR_anti_sigma_factor 62 residues - 6923.098 Da.

1

MET

LEU

ASP

LEU

PRO

GLY

ASN

LYS

ASP

LYS

2

LYS

ALA

SER

LYS

SER

PRO

ALA

LYS

3

VAL

GLN

SER

LYS

ASP

ARG

ASP

MET

GLY

ALA

4

ALA

LEU

ARG

SER

ALA

TYR

GLN

LYS

THR

ILE

5

GLU

GLN

VAL

PRO

ASP

GLU

MET

LEU

ASP

6

LEU

ASN

LYS

LEU

ALA

LEU

GLU

LEU

VAL

7

PRO

ARG

Samples:

sample_1: PhyR sigma like domain, [U-100% 13C; U-100% 15N], 0.8 ± 0.02 mM; NepR anti sigma factor 0.8 ± 0.02 mM; sodium chloride 50 ± 0.05 mM; sodium phosphate 10 ± 0.01 mM; H2O 90%; D2O 10%

sample_2: PhyR sigma like domain 0.8 ± 0.02 mM; NepR anti sigma factor, [U-100% 13C; U-100% 15N], 0.8 ± 0.02 mM; sodium chloride 50 ± 0.05 mM; sodium phosphate 10 ± 0.01 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.06 M; pH: 6.8; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

UNIO v10, (Torsten Herrmann) - peak picking

CYANA v3, CYANA (Peter Guntert) - structure solution

AMBER v8, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

TOPSPIN v2.1, Bruker Biospin - processing

Molmol v2.2K, Koradi, Billeter and Wuthrich - data analysis

PyMol v1.3, Schrodinger, LLC. - data analysis

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 900 MHz

PDB	2LFW 2LFW
GB	AET62591 KIU26946 AET62590
REF	WP_017979560 WP_043060725