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

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Basic information

Entry
Database: PDB / ID: 8plh
TitleThioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 18.
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 / 4-(5-amino-1,3,4-thiadiazol-2-yl)phenol / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2895
Polymers64,9241
Non-polymers1,3654
Water3,387188
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


  • defined by author&software
  • Evidence: homology, REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 11820 ANGSTROM**2 ...Evidence: homology, REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 11820 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 47430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 2.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 2.00000
  • 133 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)132,57810
Polymers129,8482
Non-polymers2,7308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area10600 Å2
ΔGint-75 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.154, 103.498, 62.207
Angle α, β, γ (deg.)90.000, 113.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Thioredoxin glutathione reductase


Mass: 64923.918 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GVY / 4-(5-amino-1,3,4-thiadiazol-2-yl)phenol


Mass: 193.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H7N3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.32 Å3/Da / Density % sol: 63 %
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: 1.62→29.43 Å / Num. obs: 107317 / % possible obs: 99.68 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.48
Reflection shellResolution: 1.62→1.678 Å / Num. unique obs: 10717 / CC1/2: 0.694

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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: 1.62→29.43 Å / SU ML: 0.1862 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.6062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 5409 5.04 %
Rwork0.2184 101908 -
obs0.2193 107317 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.81 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4483 0 92 188 4763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824668
X-RAY DIFFRACTIONf_angle_d0.90486332
X-RAY DIFFRACTIONf_chiral_restr0.0584718
X-RAY DIFFRACTIONf_plane_restr0.0077837
X-RAY DIFFRACTIONf_dihedral_angle_d9.7711662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.30621910.27253302X-RAY DIFFRACTION96.63
1.64-1.660.29561860.2763384X-RAY DIFFRACTION99.92
1.66-1.680.29021800.26023401X-RAY DIFFRACTION99.94
1.68-1.70.31121750.2523358X-RAY DIFFRACTION99.92
1.7-1.720.25331950.24493437X-RAY DIFFRACTION99.78
1.72-1.740.26421930.23393343X-RAY DIFFRACTION99.97
1.74-1.770.23961930.22933371X-RAY DIFFRACTION99.66
1.77-1.80.25121760.22853382X-RAY DIFFRACTION99.78
1.8-1.820.23862020.22983407X-RAY DIFFRACTION99.78
1.82-1.850.28381840.22983363X-RAY DIFFRACTION99.94
1.85-1.890.24482080.23323415X-RAY DIFFRACTION99.94
1.89-1.920.24691700.22563377X-RAY DIFFRACTION99.92
1.92-1.960.24341540.21993408X-RAY DIFFRACTION99.92
1.96-20.26471940.21623417X-RAY DIFFRACTION99.94
2-2.040.24992070.21453365X-RAY DIFFRACTION100
2.04-2.090.26471500.23133455X-RAY DIFFRACTION99.97
2.09-2.140.23391620.22713401X-RAY DIFFRACTION99.94
2.14-2.20.26551570.23443435X-RAY DIFFRACTION99.83
2.2-2.260.25582040.23673354X-RAY DIFFRACTION99.75
2.26-2.330.23971830.22483399X-RAY DIFFRACTION99.89
2.34-2.420.28881520.23813447X-RAY DIFFRACTION99.78
2.42-2.520.26571860.24333388X-RAY DIFFRACTION99.89
2.52-2.630.29061750.24483416X-RAY DIFFRACTION99.81
2.63-2.770.25491880.24333399X-RAY DIFFRACTION99.67
2.77-2.940.25441530.24743428X-RAY DIFFRACTION99.67
2.94-3.170.2611910.23253398X-RAY DIFFRACTION99.56
3.17-3.490.2461670.22313418X-RAY DIFFRACTION99.2
3.49-3.990.19271880.19883381X-RAY DIFFRACTION98.84
3.99-5.020.1571850.16973400X-RAY DIFFRACTION98.73
5.02-29.430.19331600.17353459X-RAY DIFFRACTION98.34

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