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

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Basic information

Entry
Database: PDB / ID: 8plc
TitleThioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 13.
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
(1~{R})-1-(4-ethoxyphenyl)ethanamine / FLAVIN-ADENINE DINUCLEOTIDE / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.1Nov 6, 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)131,7496
Polymers129,8482
Non-polymers1,9024
Water17,547974
1
A: Thioredoxin glutathione reductase
hetero molecules

B: 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: 10480 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: 10480 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 47480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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
  • 132 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)131,7496
Polymers129,8482
Non-polymers1,9024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area10060 Å2
ΔGint-78 kcal/mol
Surface area47610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.120, 103.290, 133.610
Angle α, β, γ (deg.)90.000, 92.030, 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-A7N / (1~{R})-1-(4-ethoxyphenyl)ethanamine


Mass: 165.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
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: 2.34→55.55 Å / Num. obs: 70234 / % possible obs: 98.16 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.61 Å2 / CC1/2: 0.967 / Net I/σ(I): 4.34
Reflection shellResolution: 2.34→2.424 Å / Num. unique obs: 6959 / CC1/2: 0.633

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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: 2.34→55.55 Å / SU ML: 0.3182 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 37.4134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 3475 4.97 %
Rwork0.2269 66428 -
obs0.229 69903 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.43 Å2
Refinement stepCycle: LAST / Resolution: 2.34→55.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 130 974 10110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00789320
X-RAY DIFFRACTIONf_angle_d0.909112644
X-RAY DIFFRACTIONf_chiral_restr0.05271442
X-RAY DIFFRACTIONf_plane_restr0.00771608
X-RAY DIFFRACTIONf_dihedral_angle_d10.23591280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.36531220.30092670X-RAY DIFFRACTION98.52
2.37-2.410.33631200.29152678X-RAY DIFFRACTION97.76
2.41-2.440.30441300.2872619X-RAY DIFFRACTION98.99
2.44-2.480.33381210.28572695X-RAY DIFFRACTION98.08
2.48-2.520.31321330.28232658X-RAY DIFFRACTION98.34
2.52-2.560.36381340.28432648X-RAY DIFFRACTION98.3
2.56-2.610.33091700.27892600X-RAY DIFFRACTION98.44
2.61-2.660.34771320.26832678X-RAY DIFFRACTION98.98
2.66-2.720.3121220.26182707X-RAY DIFFRACTION98.88
2.72-2.770.2991580.26422619X-RAY DIFFRACTION99.18
2.77-2.840.32311530.25632687X-RAY DIFFRACTION99.09
2.84-2.910.32641120.25312692X-RAY DIFFRACTION99.29
2.91-2.990.28881440.24162688X-RAY DIFFRACTION99.19
2.99-3.080.29521560.23352670X-RAY DIFFRACTION99.37
3.08-3.180.29871520.24072664X-RAY DIFFRACTION99.19
3.18-3.290.26921400.23272665X-RAY DIFFRACTION98.94
3.29-3.420.29241200.22692703X-RAY DIFFRACTION98.84
3.42-3.580.24641490.2122620X-RAY DIFFRACTION97.67
3.58-3.770.26071370.20412654X-RAY DIFFRACTION97.66
3.77-40.22311620.19742618X-RAY DIFFRACTION97.96
4-4.310.21961570.18032638X-RAY DIFFRACTION97.18
4.31-4.740.2041710.17532601X-RAY DIFFRACTION97.33
4.74-5.430.22511350.18612696X-RAY DIFFRACTION98.37
5.43-6.840.24271310.21592734X-RAY DIFFRACTION99.13
6.84-55.550.15161140.16092526X-RAY DIFFRACTION89.98

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