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

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Basic information

Entry
Database: PDB / ID: 8plq
TitleThioredoxin glutathione reductase of Schistosoma mansoni fragment screen hit 27.
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 / ~{N}-(1-ethylbenzimidazol-2-yl)ethanamide / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
B: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6225
Polymers129,8482
Non-polymers1,7743
Water16,268903
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: 10430 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: 10430 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 47630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74 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 IN ADDITION APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 1.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -0.50000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 1.
  • 132 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)131,6225
Polymers129,8482
Non-polymers1,7743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area10060 Å2
ΔGint-77 kcal/mol
Surface area47700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.301, 103.838, 134.815
Angle α, β, γ (deg.)90.000, 91.600, 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-TEK / ~{N}-(1-ethylbenzimidazol-2-yl)ethanamide


Mass: 203.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 903 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
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: 2.29→29.61 Å / Num. obs: 76578 / % possible obs: 99.12 % / Redundancy: 1.9 % / Biso Wilson estimate: 41.09 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.55
Reflection shellResolution: 2.29→2.373 Å / Num. unique obs: 7483 / CC1/2: 0.806

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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: 2.29→29.61 Å / SU ML: 0.2969 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.0498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 3810 4.98 %
Rwork0.1841 72655 -
obs0.1864 76465 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.41 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 121 903 10030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829312
X-RAY DIFFRACTIONf_angle_d0.929412636
X-RAY DIFFRACTIONf_chiral_restr0.05411440
X-RAY DIFFRACTIONf_plane_restr0.0081607
X-RAY DIFFRACTIONf_dihedral_angle_d9.96241275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.35711270.31142547X-RAY DIFFRACTION94.06
2.32-2.350.30561570.26622645X-RAY DIFFRACTION99.75
2.35-2.380.27891340.25282727X-RAY DIFFRACTION99.83
2.38-2.420.27351130.23842736X-RAY DIFFRACTION99.75
2.42-2.450.28091410.23112672X-RAY DIFFRACTION99.93
2.45-2.490.29931180.23822747X-RAY DIFFRACTION99.79
2.49-2.530.32921320.23992694X-RAY DIFFRACTION99.72
2.53-2.580.27711400.23422727X-RAY DIFFRACTION99.83
2.58-2.620.28561570.23172656X-RAY DIFFRACTION99.86
2.62-2.670.3161420.22362686X-RAY DIFFRACTION99.93
2.67-2.730.28321300.21892732X-RAY DIFFRACTION99.79
2.73-2.790.27161590.20822655X-RAY DIFFRACTION99.72
2.79-2.850.27031530.20822689X-RAY DIFFRACTION99.37
2.85-2.920.25141110.20392701X-RAY DIFFRACTION99.61
2.92-30.27031460.19762738X-RAY DIFFRACTION99.76
3-3.090.22391540.19222672X-RAY DIFFRACTION99.58
3.09-3.190.23841540.19462675X-RAY DIFFRACTION99.72
3.19-3.30.24941450.18922692X-RAY DIFFRACTION99.61
3.3-3.440.24541170.18782734X-RAY DIFFRACTION99.51
3.44-3.590.22791540.18442679X-RAY DIFFRACTION99.26
3.59-3.780.24191400.17042710X-RAY DIFFRACTION99.41
3.78-4.020.20051590.16262671X-RAY DIFFRACTION99.19
4.02-4.330.18951630.1492675X-RAY DIFFRACTION98.85
4.33-4.760.18451740.13782678X-RAY DIFFRACTION98.99
4.76-5.450.17041380.14862704X-RAY DIFFRACTION98.85
5.45-6.850.22231300.18072722X-RAY DIFFRACTION98.89
6.85-29.610.14821220.14962691X-RAY DIFFRACTION95.39

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