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- PDB-6zom: Oxidized thioredoxin 1 from the anaerobic bacteria Desulfovibrio ... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6zom
TitleOxidized thioredoxin 1 from the anaerobic bacteria Desulfovibrio vulgaris Hildenborough
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / desulfovibrio / enzyme / cystein / vulgaris / redox homeostasis / regulation / thiol / oxidized
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
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
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGarcin, E. / Bornet, O. / Nouailler, M. / Pieulle, L. / Guerlesquin, F. / Sebban-Kreuzer, C.
Citation
Journal: Extremophiles / Year: 2021
Title: Glutamate optimizes enzymatic activity under high hydrostatic pressure in Desulfovibrio species: effects on the ubiquitous thioredoxin system.
Authors: Gaussier, H. / Nouailler, M. / Champaud, E. / Garcin, E.B. / Sebban-Kreuzer, C. / Bornet, O. / Garel, M. / Tamburini, C. / Pieulle, L. / Dolla, A. / Pradel, N.
#1: Journal: Biomol NMR Assign / Year: 2011
Title: 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.
Authors: Garcin, E.B. / Bornet, O. / Pieulle, L. / Guerlesquin, F. / Sebban-Kreuzer, C.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)12,2751
Polymers12,2751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5680 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Thioredoxin


Mass: 12275.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oxidized / Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: trx, DVU_1839 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72B01
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
171isotropic13D HN(CA)CB
181isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-15N NOESY
191isotropic13D HNCA
1131isotropic13D HNHA
1121isotropic13D HBHA(CO)NH
1111isotropic13D HN(CO)CA
1141isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] Thioredoxin 1, 90% H2O/10% D2O
Details: oxidized thioredoxin, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%; NaCl 100 mM; Potassium phosphate 50 mM
Label: oxidized thioredoxin / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: Thioredoxin 1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: oxidized thioredoxin, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%; NaCl 100 mM; Potassium phosphate 50 mM
Ionic strength: 100 mM / Ionic strength err: 1 / Label: oxidized thioredoxin / pH: 5.5 / PH err: 0.01 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 290 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz / Details: cryoprobe

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxchemical shift calculation
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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