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- PDB-7jyp: Structure of thioredoxin reductase from the thermophilic eubacter... -

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Basic information

Entry
Database: PDB / ID: 7jyp
TitleStructure of thioredoxin reductase from the thermophilic eubacterium Thermosipho africanus TCF52B
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase / thermophile / Thermosipho africanus / protein stability / catalysis / NADH
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / cytoplasm
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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesThermosipho africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: To be Published
Title: Structure of thioredoxin reductase from the thermophilic eubacterium Thermosipho africanus TCF52B.
Authors: Sahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R.
#1: Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structure and function of the putative thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus strain TCF52B.
Authors: Sahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R.
#2: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Putative thioredoxin Trx1 from Thermosipho africanus strain TCF52B: expression, purification and structural determination using S-SAD.
Authors: Sahtout, N. / Kuttiyatveetil, J.R. / Fodje, M. / Sanders, D.A.
History
DepositionAug 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8933
Polymers37,4441
Non-polymers1,4492
Water1,67593
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7856
Polymers74,8872
Non-polymers2,8984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7620 Å2
ΔGint-41 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.150, 58.150, 163.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thioredoxin reductase


Mass: 37443.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho africanus (strain TCF52B) (bacteria)
Strain: TCF52B / Gene: trxB, THA_1385 / Plasmid: pEHISTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: B7ICV3, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.15 % / Description: yellow rhomboid shaped crystals
Crystal growTemperature: 289 K / Method: microbatch
Details: 0.2 M Ammonium Chloride, 20 % (w/v) PEG 3350, 0.1 M b-Nicotinamide adenine dinucleotide (NAD) hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→48.12 Å / Num. obs: 42842 / % possible obs: 99.2 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.76 Å2 / CC1/2: 0.999 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 3980 / CC1/2: 0.17 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
SCALAdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Automated

Resolution: 1.6→48.119 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 2135 4.99 %
Rwork0.2143 --
obs0.2158 42763 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→48.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 62 93 2472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072440
X-RAY DIFFRACTIONf_angle_d1.2063310
X-RAY DIFFRACTIONf_dihedral_angle_d14.0411417
X-RAY DIFFRACTIONf_chiral_restr0.082372
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.63730.56151300.54472475X-RAY DIFFRACTION93
1.6373-1.67820.56991380.53142605X-RAY DIFFRACTION96
1.6782-1.72360.50341390.48312640X-RAY DIFFRACTION99
1.7236-1.77430.42211412689X-RAY DIFFRACTION100
1.7743-1.83160.37971400.35682691X-RAY DIFFRACTION100
1.8316-1.89710.33541420.29452689X-RAY DIFFRACTION99
1.8971-1.9730.33141390.26342691X-RAY DIFFRACTION100
1.973-2.06280.26171440.21562715X-RAY DIFFRACTION100
2.0628-2.17160.23961410.20722690X-RAY DIFFRACTION100
2.1716-2.30760.24141440.19152730X-RAY DIFFRACTION100
2.3076-2.48580.25841430.19212731X-RAY DIFFRACTION100
2.4858-2.73590.24251440.19022739X-RAY DIFFRACTION100
2.7359-3.13180.24231460.19772777X-RAY DIFFRACTION100
3.1318-3.94540.18141480.18092807X-RAY DIFFRACTION100
3.9454-100.19691560.16992959X-RAY DIFFRACTION100

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