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- PDB-2x8c: Thioredoxin glutathione reductase from Schistosoma mansoni with t... -

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Basic information

Entry
Database: PDB / ID: 2x8c
TitleThioredoxin glutathione reductase from Schistosoma mansoni with the reduced C-terminal end
ComponentsTHIOREDOXIN GLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE/FLAVOPROTEIN / OXIDOREDUCTASE-FLAVOPROTEIN COMPLEX / DETOXIFICATION PATHWAY
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 / FAD/NAD-linked reductase, C-terminal dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAngelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Mapping the Catalytic Cycle of Schistosoma Mansoni Thioredoxin Glutathione Reductase by X-Ray Crystallography
Authors: Angelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A.
#1: Journal: Proteins / Year: 2008
Title: Glutathione Reductase and Thioredoxin Reductase at the Crossroad: The Structure of Schistosoma Mansoni Thioredoxin Glutathione Reductase.
Authors: Angelucci, F. / Miele, A.E. / Boumis, G. / Dimastrogiovanni, D. / Brunori, M. / Bellelli, A.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Inhibition of Schistosoma Mansoni Thioredoxin- Glutathione Reductase by Auranofin: Structural and Kinetic Aspects.
Authors: Angelucci, F. / Sayed, A.A. / Williams, D.L. / Boumis, G. / Brunori, M. / Dimastrogiovanni, D. / Miele, A.E. / Pauly, F. / Bellelli, A.
History
DepositionMar 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)132,2508
Polymers130,1222
Non-polymers2,1286
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-58.5 kcal/mol
Surface area47180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.492, 87.448, 185.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOREDOXIN GLUTATHIONE REDUCTASE


Mass: 65061.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
Sequence detailsRESIDUE 597 IS GIVEN AS X IN UNIPROT, IT IS CYS IN THIS CONSTRUCT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: VAPOR DIFFUSION, SITTING DROP, 0.2 M MG-FORMATE, 20% PEG 6000, 0.1 M SODIUM HEPES, PH 7.0-7.5, TEMP 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 24223 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6O

2v6o


Resolution: 3.1→92.76 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.828 / SU B: 23.351 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5 AND 594-598 OF CHAIN A AND RESIDUES 1-5 OF CHAIN B ARE NOT VISIBLE BY THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.29257 1299 5.1 %RANDOM
Rwork0.21606 ---
obs0.21995 24223 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--1.64 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 3.1→92.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9033 0 143 0 9176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229347
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.98112667
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65551177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00424.851369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.536151598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9521534
X-RAY DIFFRACTIONr_chiral_restr0.0760.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216892
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.41.55828
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74729393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.77833519
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3914.53274
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.097→3.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 96 -
Rwork0.265 1720 -
obs--98.16 %

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