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- PDB-2l59: Solution Structures of Oxidized and Reduced Thioredoxin C from M. tb -

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Basic information

Entry
Database: PDB / ID: 2l59
TitleSolution Structures of Oxidized and Reduced Thioredoxin C from M. tb
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / Trx / M. tb / Tuberculosis / TrxC
Function / homology
Function and homology information


Cysteine synthesis from O-acetylserine / Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / peptidoglycan-based cell wall / electron transfer activity / extracellular region ...Cysteine synthesis from O-acetylserine / Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / peptidoglycan-based cell wall / electron transfer activity / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / Thioredoxin
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 16
AuthorsOlson, A.L. / Cai, S. / Sem, D.S.
CitationJournal: Proteins / Year: 2013
Title: Solution structures of Mycobacterium tuberculosis thioredoxin C and models of intact thioredoxin system suggest new approaches to inhibitor and drug design.
Authors: Olson, A.L. / Neumann, T.S. / Cai, S. / Sem, D.S.
History
DepositionOct 28, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Apr 3, 2013Group: Database references

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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)12,5571
Polymers12,5571
Non-polymers00
Water00
1


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

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Components

#1: Protein Thioredoxin / Trx / MPT46


Mass: 12557.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trxA, trx, trxC, Rv3914, MT4033, MTV028.05 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A616, UniProt: P9WG67*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D C(CO)NH
1313D HNCA
1413D HN(CO)CA
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 50 mM potassium phosphate-1, 1.2 mM [U-13C, U-15N] Thioredoxin, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphate-11
1.2 mMThioredoxin[U-13C; U-15N]1
Sample conditionsIonic strength: 0.05 / pH: 6.3 / Pressure: ambient / Temperature: 298.4 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
NMRViewJohnson, One Moon Scientificdata analysis
SPARKYGoddarddata analysis
SPARKYGoddardchemical shift assignment
SPARKYGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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