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- PDB-2n5a: Structures of the REDUCED state of the mutant D24A of yeast thior... -

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Basic information

Entry
Database: PDB / ID: 2n5a
TitleStructures of the REDUCED state of the mutant D24A of yeast thioredoxin 1
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / Redox Catalytic Activity / Water Cavity / Protein Hydration
Function / homology
Function and homology information


membrane fusion priming complex / protein deglutathionylation / vacuole inheritance / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport ...membrane fusion priming complex / protein deglutathionylation / vacuole inheritance / vacuole fusion, non-autophagic / disulfide oxidoreductase activity / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / cell redox homeostasis / mitochondrial intermembrane space / protein transport / Golgi membrane / mitochondrion / nucleus / 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
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsIqbal, A. / Moraes, A.H. / Valente, A.P. / Almeida, F.C.L.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insights into the mechanism for the closing of the water cavity.
Authors: Iqbal, A. / Moraes, A.H. / Valente, A.P. / Almeida, F.C.
History
DepositionJul 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,2011
Polymers11,2011
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 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thioredoxin-1 / / Thioredoxin I / TR-I / Thioredoxin-2


Mass: 11200.922 Da / Num. of mol.: 1 / Mutation: D24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: TRX1, TRX2, YLR043C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22217

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D HBHA(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
NMR detailsText: TORSION ANGLE SIMULATED ANNEALING

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Sample preparation

DetailsContents: 850 uM [U-100% 13C; U-100% 15N] yTrx1D24A reduced, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 850 uM / Component: yTrx1D24A reduced-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.02 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance7002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1304 / NOE intraresidue total count: 422 / NOE long range total count: 209 / NOE medium range total count: 42 / NOE sequential total count: 253 / Protein phi angle constraints total count: 88 / Protein psi angle constraints total count: 88
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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