BMRB Entry 30025

Name: Solution structure of the BeF3-activated conformation of SdrG from Pseudomonas melonis Fr1
Published: 2016-07-13

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PDB ID: 5iej
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30025
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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 the BeF3-activated conformation of SdrG from Pseudomonas melonis Fr1

Deposition date:

2016-02-25

Original release date:

2016-07-13

Authors:

Campagne, S.; Vorholt, J.; Allain, F.H.-T.

Citation:

Citation: Campagne, Sebastien; Dintner, Sebastian; Gottschlich, Lisa; Thibault, Maxence; Bortfeld-Miller, Miriam; Kaczmarczyk, Andreas; Francez-Charlot, Anne; Allain, Frederic; Vorholt, Julia. "Role of the PFXFATG[G/Y] Motif in the Activation of SdrG, a Response Regulator Involved in the Alphaproteobacterial General Stress Response" Structure 24, 1237-1247 (2016).
PubMed: 27396826

Assembly members:

Assembly members:
SdrG, polymer, 130 residues, 13892.781 Da.

Natural source:

Natural source: Common Name: a-proteobacteria Taxonomy ID: 1090317 Superkingdom: Bacteria Kingdom: not available Genus/species: Sphingomonas Sphingomonas melonis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SdrG: MSALTQILIVEDEPLIAMML EDFLEVLDKTPVGTVDTVAG ALARVEDGGIDAAILDVNLR GGEKSTPVAEALAARDIPFV FATGGSDDSVDSRFRDRPVL QKPFTMDGVAKALAALLVPR GSVEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	499
15N chemical shifts	121
1H chemical shifts	855

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 130 residues - 13892.781 Da.

1	MET	SER	ALA	LEU	THR	GLN	ILE	LEU	ILE	VAL
2	GLU	ASP	GLU	PRO	LEU	ILE	ALA	MET	MET	LEU
3	GLU	ASP	PHE	LEU	GLU	VAL	LEU	ASP	LYS	THR
4	PRO	VAL	GLY	THR	VAL	ASP	THR	VAL	ALA	GLY
5	ALA	LEU	ALA	ARG	VAL	GLU	ASP	GLY	GLY	ILE
6	ASP	ALA	ALA	ILE	LEU	ASP	VAL	ASN	LEU	ARG
7	GLY	GLY	GLU	LYS	SER	THR	PRO	VAL	ALA	GLU
8	ALA	LEU	ALA	ALA	ARG	ASP	ILE	PRO	PHE	VAL
9	PHE	ALA	THR	GLY	GLY	SER	ASP	ASP	SER	VAL
10	ASP	SER	ARG	PHE	ARG	ASP	ARG	PRO	VAL	LEU
11	GLN	LYS	PRO	PHE	THR	MET	ASP	GLY	VAL	ALA
12	LYS	ALA	LEU	ALA	ALA	LEU	LEU	VAL	PRO	ARG
13	GLY	SER	VAL	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Samples:

sample_1: BeF3-activated conformation of SdrG, [U-99% 13C; U-99% 15N], 1 mM; beryllium Chloride 5 mM; magnesium chloride 10 mM; sodium chloride 50 mM; sodium fluoride 30 mM; sodium phosphate 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 105 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D H	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 HNCO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

AMBER12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CARA v3.96, Keller and Wuthrich - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

TOPSPIN v3.96, Bruker Biospin - collection

NMR spectrometers:

Bruker AvanceIII 500 MHz
Bruker Avance 900 MHz

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

1	MET	SER	ALA	LEU	THR	GLN	ILE	LEU	ILE	VAL
2	GLU	ASP	GLU	PRO	LEU	ILE	ALA	MET	MET	LEU
3	GLU	ASP	PHE	LEU	GLU	VAL	LEU	ASP	LYS	THR
4	PRO	VAL	GLY	THR	VAL	ASP	THR	VAL	ALA	GLY
5	ALA	LEU	ALA	ARG	VAL	GLU	ASP	GLY	GLY	ILE
6	ASP	ALA	ALA	ILE	LEU	ASP	VAL	ASN	LEU	ARG
7	GLY	GLY	GLU	LYS	SER	THR	PRO	VAL	ALA	GLU
8	ALA	LEU	ALA	ALA	ARG	ASP	ILE	PRO	PHE	VAL
9	PHE	ALA	THR	GLY	GLY	SER	ASP	ASP	SER	VAL
10	ASP	SER	ARG	PHE	ARG	ASP	ARG	PRO	VAL	LEU
11	GLN	LYS	PRO	PHE	THR	MET	ASP	GLY	VAL	ALA
12	LYS	ALA	LEU	ALA	ALA	LEU	LEU	VAL	PRO	ARG
13	GLY	SER	VAL	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	MET	SER	ALA	LEU	THR	GLN	ILE	LEU	ILE	VAL
2	GLU	ASP	GLU	PRO	LEU	ILE	ALA	MET	MET	LEU
3	GLU	ASP	PHE	LEU	GLU	VAL	LEU	ASP	LYS	THR
4	PRO	VAL	GLY	THR	VAL	ASP	THR	VAL	ALA	GLY
5	ALA	LEU	ALA	ARG	VAL	GLU	ASP	GLY	GLY	ILE
6	ASP	ALA	ALA	ILE	LEU	ASP	VAL	ASN	LEU	ARG
7	GLY	GLY	GLU	LYS	SER	THR	PRO	VAL	ALA	GLU
8	ALA	LEU	ALA	ALA	ARG	ASP	ILE	PRO	PHE	VAL
9	PHE	ALA	THR	GLY	GLY	SER	ASP	ASP	SER	VAL
10	ASP	SER	ARG	PHE	ARG	ASP	ARG	PRO	VAL	LEU
11	GLN	LYS	PRO	PHE	THR	MET	ASP	GLY	VAL	ALA
12	LYS	ALA	LEU	ALA	ALA	LEU	LEU	VAL	PRO	ARG
13	GLY	SER	VAL	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	MET	SER	ALA	LEU	THR	GLN	ILE	LEU	ILE	VAL
2	GLU	ASP	GLU	PRO	LEU	ILE	ALA	MET	MET	LEU
3	GLU	ASP	PHE	LEU	GLU	VAL	LEU	ASP	LYS	THR
4	PRO	VAL	GLY	THR	VAL	ASP	THR	VAL	ALA	GLY
5	ALA	LEU	ALA	ARG	VAL	GLU	ASP	GLY	GLY	ILE
6	ASP	ALA	ALA	ILE	LEU	ASP	VAL	ASN	LEU	ARG
7	GLY	GLY	GLU	LYS	SER	THR	PRO	VAL	ALA	GLU
8	ALA	LEU	ALA	ALA	ARG	ASP	ILE	PRO	PHE	VAL
9	PHE	ALA	THR	GLY	GLY	SER	ASP	ASP	SER	VAL
10	ASP	SER	ARG	PHE	ARG	ASP	ARG	PRO	VAL	LEU
11	GLN	LYS	PRO	PHE	THR	MET	ASP	GLY	VAL	ALA
12	LYS	ALA	LEU	ALA	ALA	LEU	LEU	VAL	PRO	ARG
13	GLY	SER	VAL	GLU	HIS	HIS	HIS	HIS	HIS	HIS