BMRB Entry 30290

Name: NMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)155
Published: 2017-06-02

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PDB ID: 5vo7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30290
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:

NMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)155

Deposition date:

2017-05-02

Original release date:

2017-06-02

Authors:

Barnwal, R.; Varani, G.; Seattle Structural Genomics Center for Infectious Disease (SSGCID), SSGCID

Citation:

Citation: Barnwal, R.; Varani, G.. "Assignment and Structure of Thioredoxin (Rv1471 ortholog) type protein from Mycobacterium smegmatis ATCC 700084 / mc(2)155" .

Assembly members:

Assembly members:
entity_1, polymer, 110 residues, 11634.341 Da.

Natural source:

Natural source: Common Name: Mycobacterium smegmatis Taxonomy ID: 1772 Superkingdom: Bacteria Kingdom: not available Genus/species: Mycobacterium smegmatis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MSEDSATVAVTDDSFSTDVL GSSKPVLVDFWATWCGPCKM VAPVLEEIAAEKGDQLTVAK IDVDANPATARDFQVVSIPT MILFKDGAPVKRIVGAKGKA ALLRELSDAL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	448
15N chemical shifts	105
1H chemical shifts	661

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_1 110 residues - 11634.341 Da.

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

Samples:

sample_1: Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C, [U-99% 13C; U-99% 15N], 1.1 ± 0.1 mM; NaCl 100 mM

sample_conditions_1: ionic strength: 100 mM; 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
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

Analysis, CCPN - chemical shift assignment

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

CcpNMR, CCPN - data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceII 600 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	GLU	ASP	SER	ALA	THR	VAL	ALA	VAL
2	THR	ASP	ASP	SER	PHE	SER	THR	ASP	VAL	LEU
3	GLY	SER	SER	LYS	PRO	VAL	LEU	VAL	ASP	PHE
4	TRP	ALA	THR	TRP	CYS	GLY	PRO	CYS	LYS	MET
5	VAL	ALA	PRO	VAL	LEU	GLU	GLU	ILE	ALA	ALA
6	GLU	LYS	GLY	ASP	GLN	LEU	THR	VAL	ALA	LYS
7	ILE	ASP	VAL	ASP	ALA	ASN	PRO	ALA	THR	ALA
8	ARG	ASP	PHE	GLN	VAL	VAL	SER	ILE	PRO	THR
9	MET	ILE	LEU	PHE	LYS	ASP	GLY	ALA	PRO	VAL
10	LYS	ARG	ILE	VAL	GLY	ALA	LYS	GLY	LYS	ALA
11	ALA	LEU	LEU	ARG	GLU	LEU	SER	ASP	ALA	LEU

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

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