BMRB Entry 18443

Name: Solution structure of a thioredoxin from Thermus thermophilus
Published: 2012-06-05

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PDB ID: 2lst
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18443
MolProbity Validation Chart

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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:

Solution structure of a thioredoxin from Thermus thermophilus

Deposition date:

2012-05-04

Original release date:

2012-06-05

Authors:

Harris, R.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.

Citation:

Citation: Harris, R.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.. "Solution structure of a thioredoxin from Thermus thermophilus" To be published ., .-..

Assembly members:

Assembly members:
thioredoxin, polymer, 130 residues, 14740.037 Da.

Natural source:

Natural source: Common Name: bacteria Taxonomy ID: 274 Superkingdom: Bacteria Kingdom: not available Genus/species: Thermus thermophilus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: modified pET26

Entity Sequences (FASTA):

Entity Sequences (FASTA):
thioredoxin: MSLRWYPYPEALALAQAHGR MVMVYFHSEHCPYCQQMNTF VLSDPGVSRLLEARFVVASV SVDTPEGQELARRYRVPGTP TFVFLVPKAGAWEEVGRLFG SRPRAEFLKELRQVCVKGGA CGEGHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	547
15N chemical shifts	121
1H chemical shifts	848

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	thioredoxin	1

Entities:

Entity 1, thioredoxin 130 residues - 14740.037 Da.

expressed sequence start-stop 35-153 (130 aa incl tag) N-term cloning artifact: MSL C-term cloning artifact: EGHHHHHH

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

Samples:

sample_1: thioredoxin, [U-13C; U-15N], 0.5 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 5 mM; EDTA 1 mM

sample_2: thioredoxin, [U-13C; U-15N], 0.5 mM; sodium phosphate 20 mM; sodium chloride 50 mM; DTT 5 mM; EDTA 1 mM

sample_conditions_1: ionic strength: 70 mM; pH: 5.8; pressure: 1 ATM; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N HSQC	sample_1	isotropic	sample_conditions_1
15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
13C HSQC	sample_2	isotropic	sample_conditions_1
aromatic 13C HSQC	sample_2	isotropic	sample_conditions_1
13C NOESY-HSQC	sample_2	isotropic	sample_conditions_1
13C aromatic NOESY-HSQC	sample_2	isotropic	sample_conditions_1
HNCO	sample_1	isotropic	sample_conditions_1
HNCACO	sample_1	isotropic	sample_conditions_1
HNCA	sample_1	isotropic	sample_conditions_1
HNCOCA	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1

Software:

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

ARIA v2.3, Linge, O'Donoghue and Nilges - data analysis

CCPN v2.1.5, CCPN - chemical shift assignment, data analysis, peak picking

NMRPipe v5.4, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMRJ v2.2D, Varian - collection

TOPSPIN v1.3, Bruker Biospin - collection

MDDNMR v2.0, (MDDNMR) Orekhov, Jaravine, Kazimierczuk - collection, processing

MDDGUI v1.0, (MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith - collection, processing

SIDER, Hansen - data analysis

NMR spectrometers:

Varian Inova 600 MHz
Bruker Avance 600 MHz

PDB	2LST
DBJ	BAD71245
GB	AAS81399 AEG33835 AFH38530
REF	WP_011228670 WP_024119461 WP_041443497 WP_041445022 YP_144688

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

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