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- PDB-8pdd: Thioredoxin glutathione reductase of Schistosoma mansoni at 1.25A... -

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Basic information

Entry
Database: PDB / ID: 8pdd
TitleThioredoxin glutathione reductase of Schistosoma mansoni at 1.25A resolution.
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Bi-functional / Oxidoreductase / Homodimer
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / flavin adenine dinucleotide binding / metal ion binding
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 / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 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 12, 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)132,87322
Polymers129,8482
Non-polymers3,02520
Water25,1491396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14160 Å2
ΔGint-104 kcal/mol
Surface area46180 Å2
Unit cell
Length a, b, c (Å)61.900, 102.400, 131.460
Angle α, β, γ (deg.)90.000, 92.390, 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1396 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tris pH 8.5, 0.2 M magnesium chloride, 15 % w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.25→61.85 Å / Num. obs: 450219 / % possible obs: 99.93 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.51 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.71
Reflection shellResolution: 1.25→1.295 Å / Num. unique obs: 44965 / CC1/2: 0.544

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Processing

Software
NameVersionClassification
xia2data scaling
xia2data reduction
autoSHARPphasing
REFMAC5.8.0158refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 1.25→61.85 Å / SU ML: 0.1171 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.4029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1627 22369 4.97 %
Rwork0.1429 427850 -
obs0.1439 450219 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.11 Å2
Refinement stepCycle: LAST / Resolution: 1.25→61.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 199 1396 10601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00559946
X-RAY DIFFRACTIONf_angle_d0.899313588
X-RAY DIFFRACTIONf_chiral_restr0.08771535
X-RAY DIFFRACTIONf_plane_restr0.00821725
X-RAY DIFFRACTIONf_dihedral_angle_d9.94661457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.28197560.260714358X-RAY DIFFRACTION99.92
1.26-1.280.2667850.245214041X-RAY DIFFRACTION99.97
1.28-1.290.25626650.233714360X-RAY DIFFRACTION99.98
1.29-1.310.23577160.218914273X-RAY DIFFRACTION99.99
1.31-1.330.22647080.199314249X-RAY DIFFRACTION99.98
1.33-1.350.21387590.193114227X-RAY DIFFRACTION99.98
1.35-1.370.21567200.184914205X-RAY DIFFRACTION99.99
1.37-1.390.19996940.174514337X-RAY DIFFRACTION99.98
1.39-1.410.18498130.164814183X-RAY DIFFRACTION100
1.41-1.430.17787500.154114171X-RAY DIFFRACTION99.99
1.43-1.460.17327180.147414224X-RAY DIFFRACTION99.98
1.46-1.480.17147640.142814234X-RAY DIFFRACTION99.97
1.48-1.510.16297740.138414280X-RAY DIFFRACTION99.98
1.51-1.540.15047410.129614200X-RAY DIFFRACTION99.97
1.54-1.570.15657360.12614310X-RAY DIFFRACTION99.99
1.57-1.610.14567550.120814181X-RAY DIFFRACTION99.99
1.61-1.650.14667540.117214243X-RAY DIFFRACTION100
1.65-1.70.14777600.119114235X-RAY DIFFRACTION99.98
1.7-1.750.14097410.117114233X-RAY DIFFRACTION99.98
1.75-1.80.14957050.124914345X-RAY DIFFRACTION99.99
1.8-1.870.15297880.126514236X-RAY DIFFRACTION100
1.87-1.940.1527740.131914222X-RAY DIFFRACTION99.97
1.94-2.030.15067730.127714262X-RAY DIFFRACTION99.95
2.03-2.140.15217600.131714306X-RAY DIFFRACTION99.89
2.14-2.270.15097140.135614274X-RAY DIFFRACTION99.92
2.27-2.450.15447880.141114213X-RAY DIFFRACTION99.95
2.45-2.690.17217470.150814351X-RAY DIFFRACTION99.89
2.69-3.080.16267520.148814290X-RAY DIFFRACTION99.85
3.08-3.880.1587250.138614370X-RAY DIFFRACTION99.7
3.88-61.850.15547340.139814437X-RAY DIFFRACTION99.2

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