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- PDB-3f8p: Structure of Sulfolobus solfataricus TrxR-B3 -

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Basic information

Entry
Database: PDB / ID: 3f8p
TitleStructure of Sulfolobus solfataricus TrxR-B3
ComponentsThioredoxin reductase (TrxB-3)
KeywordsOXIDOREDUCTASE / Redox protein / nucleotide binding / FAD / Flavoprotein
Function / homology
Function and homology information


NADH dehydrogenase / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH oxidase/thioredoxin reductase / Thioredoxin reductase (TrxB-3)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRuggiero, A. / Masullo, M. / Ruocco, M.R. / Arcari, P. / Zagari, A. / Vitagliano, L.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Structure and stability of a thioredoxin reductase from Sulfolobus solfataricus: a thermostable protein with two functions
Authors: Ruggiero, A. / Masullo, M. / Ruocco, M.R. / Grimaldi, P. / Lanzotti, M.A. / Arcari, P. / Zagari, A. / Vitagliano, L.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase (TrxB-3)
B: Thioredoxin reductase (TrxB-3)
C: Thioredoxin reductase (TrxB-3)
D: Thioredoxin reductase (TrxB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,35715
Polymers141,0674
Non-polymers3,29011
Water5,405300
1
A: Thioredoxin reductase (TrxB-3)
B: Thioredoxin reductase (TrxB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,40110
Polymers70,5332
Non-polymers1,8678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-112 kcal/mol
Surface area24690 Å2
MethodPISA
2
C: Thioredoxin reductase (TrxB-3)
D: Thioredoxin reductase (TrxB-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9565
Polymers70,5332
Non-polymers1,4233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-51 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.766, 120.678, 126.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thioredoxin reductase (TrxB-3)


Mass: 35266.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pET-28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97W27, UniProt: Q8X236*PLUS, EC: 1.6.4.5
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 12-15% (w/v) poly-ethylene glycol 2000 monomethyl ether, 0.1M (NH4)2SO4, 50mM sodium acetate (pH 4.6), Protein 4-9 mg/ml, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2003
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 108800 / Num. obs: 108800 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.32 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a Se-Derivative of the protein (not deposited)

Resolution: 1.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.237 8598 Random
Rwork0.2 --
all0.205 --
obs0.205 106896 -
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 137 304 9901

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