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- PDB-2lst: Solution structure of a thioredoxin from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2lst
TitleSolution structure of a thioredoxin from Thermus thermophilus
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / New York Structural Genomics Research Consortium / PSI-Biology / NYSGRC
Function / homology
Function and homology information


SoxW family / UAS / UAS / Thioredoxin-like / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulating annealing
Model detailslowest energy, model 1
AuthorsHarris, R. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. ...Harris, R. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. / Garforth, S. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Lim, S. / Love, J. / Matikainen, B. / Patel, H. / Seidel, R.D. / Smith, B. / Stead, M. / Girvin, M.E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Solution structure of a thioredoxin from Thermus thermophilus
Authors: Harris, R. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. / Garforth, S. / Gizzi, A. / Hillerich, B. / ...Authors: Harris, R. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. / Garforth, S. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Lim, S. / Love, J. / Matikainen, B. / Patel, H. / Seidel, R.D. / Smith, B. / Stead, M. / Girvin, M.E. / Almo, S.C.
History
DepositionMay 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)14,7401
Polymers14,7401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thioredoxin /


Mass: 14739.916 Da / Num. of mol.: 1 / Fragment: UNP residues 35-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1057 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72IS5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12115N NOESY-HSQC
13213C HSQC
142aromatic 13C HSQC
15213C NOESY-HSQC
16213C aromatic NOESY-HSQC
171HNCO
181HN(CA)CO
191HNCA
1101HN(CO)CA
1111HN(CA)CB
1121CBCA(CO)NH
NMR detailsText: All 3Ds collected using Non-Uniform Sampling with the MDDNMR and MDDGUI programs

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] thioredoxin, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 1 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] thioredoxin, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM DTT, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMthioredoxin-1[U-13C; U-15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMDTT-41
1 mMEDTA-51
0.5 mMthioredoxin-6[U-13C; U-15N]2
20 mMsodium phosphate-72
50 mMsodium chloride-82
5 mMDTT-92
1 mMEDTA-102
Sample conditionsIonic strength: 70 / pH: 5.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesdata analysis
CCPN2.1.5CCPNdata analysis
CCPN2.1.5CCPNpeak picking
CCPN2.1.5CCPNchemical shift assignment
NMRPipe5.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJ2.2DVariancollection
TopSpin1.3Bruker Biospincollection
MddNMR2(MDDNMR) Orekhov, Jaravine, Kazimierczukcollection
MddNMR2(MDDNMR) Orekhov, Jaravine, Kazimierczukprocessing
MDDGUI1(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmithcollection
MDDGUI1(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmithprocessing
SideRHansendata analysis
RefinementMethod: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water
NMR constraintsNOE constraints total: 2100 / NOE intraresidue total count: 553 / NOE long range total count: 598 / NOE medium range total count: 405 / NOE sequential total count: 494 / Hydrogen bond constraints total count: 47 / Protein other angle constraints total count: 31 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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