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- PDB-8plo: Thioredoxin glutathione reductase of Schistosoma mansoni fragment... -

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Basic information

Entry
Database: PDB / ID: 8plo
TitleThioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 25.
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Bi-functional / Oxidoreductase / Homodimer
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-WLY / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRibeiro, L. / Montoya, B.O. / Moreira-Filho, J.T. / Bowyer, S. / Verma, A. / Neves, B.J. / Owens, R.J. / Andrade, C.H. / Silva-Jr, F.P. / Furnham, N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026221/1 United Kingdom
Other government
Medical Research Council (MRC, United Kingdom)MR/K018779/1 United Kingdom
CitationJournal: Sci Rep / Year: 2024
Title: Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni.
Authors: de Souza Neto, L.R. / Montoya, B.O. / Brandao-Neto, J. / Verma, A. / Bowyer, S. / Moreira-Filho, J.T. / Dantas, R.F. / Neves, B.J. / Andrade, C.H. / von Delft, F. / Owens, R.J. / Furnham, N. / Silva-Jr, F.P.
History
DepositionJun 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin glutathione reductase
B: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1197
Polymers129,8482
Non-polymers2,2715
Water14,142785
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-75 kcal/mol
Surface area48120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.140, 103.560, 134.420
Angle α, β, γ (deg.)90.000, 91.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Thioredoxin glutathione reductase


Mass: 64923.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: TGR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q962Y6, EC: 1.6.4.5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-WLY / 2-(4-methylphenyl)-N-{[(2S)-oxolan-2-yl]methyl}acetamide


Mass: 233.306 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H19NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Calcium chloride dihydrate, 0.1 M Magnesium chloride hexahydrate, 0.1 M PIPES pH 7.0 and 22.5 % v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.74→62.11 Å / Num. obs: 173699 / % possible obs: 99.68 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.03
Reflection shellResolution: 1.74→1.802 Å / Num. unique obs: 17313 / CC1/2: 0.518

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→62.11 Å / SU ML: 0.2149 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.9651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 8517 4.91 %
Rwork0.2096 164960 -
obs0.2107 173477 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.99 Å2
Refinement stepCycle: LAST / Resolution: 1.74→62.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8978 0 157 785 9920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00879319
X-RAY DIFFRACTIONf_angle_d0.923612638
X-RAY DIFFRACTIONf_chiral_restr0.05961440
X-RAY DIFFRACTIONf_plane_restr0.00771612
X-RAY DIFFRACTIONf_dihedral_angle_d10.11741302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.35973120.33195452X-RAY DIFFRACTION99.86
1.76-1.780.3442710.31975512X-RAY DIFFRACTION99.74
1.78-1.80.3352970.30595469X-RAY DIFFRACTION99.91
1.8-1.830.29283050.29575496X-RAY DIFFRACTION99.93
1.83-1.850.33382580.28795474X-RAY DIFFRACTION99.95
1.85-1.870.33352580.28595513X-RAY DIFFRACTION99.95
1.87-1.90.30742700.27545524X-RAY DIFFRACTION99.97
1.9-1.930.28492660.26145500X-RAY DIFFRACTION99.91
1.93-1.960.25922870.24515491X-RAY DIFFRACTION99.93
1.96-1.990.24412670.23135521X-RAY DIFFRACTION99.93
1.99-2.030.26622510.22655531X-RAY DIFFRACTION99.95
2.03-2.060.22992720.22645521X-RAY DIFFRACTION99.9
2.06-2.10.24482570.22355472X-RAY DIFFRACTION99.88
2.1-2.150.24582750.22345575X-RAY DIFFRACTION99.9
2.15-2.190.26612820.2245452X-RAY DIFFRACTION99.86
2.19-2.240.25332830.21885542X-RAY DIFFRACTION99.98
2.24-2.30.23882690.2075514X-RAY DIFFRACTION99.88
2.3-2.360.24452960.20255481X-RAY DIFFRACTION99.78
2.36-2.430.2412620.20685482X-RAY DIFFRACTION99.88
2.43-2.510.25282970.21315514X-RAY DIFFRACTION99.88
2.51-2.60.2443050.21595502X-RAY DIFFRACTION99.74
2.6-2.70.24552790.21095523X-RAY DIFFRACTION99.81
2.7-2.830.22392890.21275477X-RAY DIFFRACTION99.79
2.83-2.980.24033230.21545453X-RAY DIFFRACTION99.57
2.98-3.160.24572840.20885489X-RAY DIFFRACTION99.6
3.16-3.410.21052790.20315539X-RAY DIFFRACTION99.78
3.41-3.750.21063470.19665456X-RAY DIFFRACTION99.62
3.75-4.290.19052810.17185538X-RAY DIFFRACTION99.49
4.29-5.410.17493270.1615490X-RAY DIFFRACTION99.3
5.41-62.110.18332680.17825457X-RAY DIFFRACTION96.04

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