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- PDB-8pl5: Thioredoxin glutathione reductase of Schistosoma mansoni fragment... -

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Basic information

Entry
Database: PDB / ID: 8pl5
TitleThioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 6.
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Bi-functional / Oxidoreductase / Homodimer
Function / homology
Function and homology information


thioredoxin-disulfide reductase / 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 / 1-[4-(cyclopropylamino)piperidin-1-yl]ethanone / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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)132,1488
Polymers129,8482
Non-polymers2,3006
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-77 kcal/mol
Surface area47880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.544, 103.623, 133.760
Angle α, β, γ (deg.)90.000, 92.170, 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-ZM8 / 1-[4-(cyclopropylamino)piperidin-1-yl]ethanone


Mass: 182.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
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: 2.15→62.5 Å / Num. obs: 92954 / % possible obs: 99.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.55 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.85
Reflection shellResolution: 2.15→2.227 Å / Num. unique obs: 9202 / CC1/2: 0.772

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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: 2.15→62.5 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 4670 5.07 %
Rwork0.1983 87427 -
obs0.2001 92097 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.97 Å2
Refinement stepCycle: LAST / Resolution: 2.15→62.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 158 722 9886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00849352
X-RAY DIFFRACTIONf_angle_d0.900112690
X-RAY DIFFRACTIONf_chiral_restr0.05691448
X-RAY DIFFRACTIONf_plane_restr0.00791594
X-RAY DIFFRACTIONf_dihedral_angle_d10.521306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.34191730.28882882X-RAY DIFFRACTION99.54
2.17-2.20.33771490.27682931X-RAY DIFFRACTION99.74
2.2-2.220.28361470.26592942X-RAY DIFFRACTION99.58
2.22-2.250.29641460.26082910X-RAY DIFFRACTION99.64
2.25-2.280.31341420.24792859X-RAY DIFFRACTION97.85
2.28-2.310.27331510.24182951X-RAY DIFFRACTION99.45
2.31-2.350.24671620.22542921X-RAY DIFFRACTION99.55
2.35-2.380.28861410.22432920X-RAY DIFFRACTION99.74
2.38-2.420.28311490.2182951X-RAY DIFFRACTION99.84
2.42-2.460.30621400.22752909X-RAY DIFFRACTION99.8
2.46-2.50.291610.22712920X-RAY DIFFRACTION99.71
2.5-2.550.28481650.22792882X-RAY DIFFRACTION99.84
2.55-2.60.2441510.22062977X-RAY DIFFRACTION99.87
2.6-2.650.27151530.21962898X-RAY DIFFRACTION99.87
2.65-2.710.25651510.21792941X-RAY DIFFRACTION99.01
2.71-2.770.26781590.21732885X-RAY DIFFRACTION99.64
2.77-2.840.25851520.21062965X-RAY DIFFRACTION99.68
2.84-2.920.25911710.20822895X-RAY DIFFRACTION99.74
2.92-30.23161680.2062918X-RAY DIFFRACTION99.64
3-3.10.22141490.21022941X-RAY DIFFRACTION99.55
3.1-3.210.25451550.21232889X-RAY DIFFRACTION99.57
3.21-3.340.24841450.2072965X-RAY DIFFRACTION99.42
3.34-3.490.22671690.20462896X-RAY DIFFRACTION98.84
3.49-3.670.28161770.19322899X-RAY DIFFRACTION98.75
3.67-3.90.19131710.1852885X-RAY DIFFRACTION98.3
3.9-4.20.20491450.16092876X-RAY DIFFRACTION97.86
4.2-4.630.16671780.1442905X-RAY DIFFRACTION98.88
4.63-5.30.16091680.14452931X-RAY DIFFRACTION99.14
5.3-6.670.20031650.18332937X-RAY DIFFRACTION98.88
6.67-62.50.17311170.15412846X-RAY DIFFRACTION92.65

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