BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18443

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts547
15N chemical shifts121
1H chemical shifts848

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1thioredoxin1

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   METSERLEUARGTRPTYRPROTYRPROGLU
2   ALALEUALALEUALAGLNALAHISGLYARG
3   METVALMETVALTYRPHEHISSERGLUHIS
4   CYSPROTYRCYSGLNGLNMETASNTHRPHE
5   VALLEUSERASPPROGLYVALSERARGLEU
6   LEUGLUALAARGPHEVALVALALASERVAL
7   SERVALASPTHRPROGLUGLYGLNGLULEU
8   ALAARGARGTYRARGVALPROGLYTHRPRO
9   THRPHEVALPHELEUVALPROLYSALAGLY
10   ALATRPGLUGLUVALGLYARGLEUPHEGLY
11   SERARGPROARGALAGLUPHELEULYSGLU
12   LEUARGGLNVALCYSVALLYSGLYGLYALA
13   CYSGLYGLUGLYHISHISHISHISHISHIS

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:

NameSampleSample stateSample conditions
15N HSQCsample_1isotropicsample_conditions_1
15N NOESY-HSQCsample_1isotropicsample_conditions_1
13C HSQCsample_2isotropicsample_conditions_1
aromatic 13C HSQCsample_2isotropicsample_conditions_1
13C NOESY-HSQCsample_2isotropicsample_conditions_1
13C aromatic NOESY-HSQCsample_2isotropicsample_conditions_1
HNCOsample_1isotropicsample_conditions_1
HNCACOsample_1isotropicsample_conditions_1
HNCAsample_1isotropicsample_conditions_1
HNCOCAsample_1isotropicsample_conditions_1
HNCACBsample_1isotropicsample_conditions_1
CBCACONHsample_1isotropicsample_conditions_1

Software:

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

ARIA v2.3, Linge, O, . - 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

Related Database Links:

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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts