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- PDB-3h4k: Crystal structure of the wild type Thioredoxin glutatione reducta... -

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Basic information

Entry
Database: PDB / ID: 3h4k
TitleCrystal structure of the wild type Thioredoxin glutatione reductase from Schistosoma mansoni in complex with auranofin
ComponentsThioredoxin glutathione reductase
KeywordsOXIDOREDUCTASE / Schistosoma mansoni / gold / Auranofin / glutathione / FAD / Flavoprotein / Redox-active center
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 / 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 / GLUTATHIONE / : / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsAngelucci, F. / Dimastrogiovanni, D. / Miele, A.E. / Boumis, G. / Brunori, M. / Bellelli, A.
CitationJournal: 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
DepositionApr 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Advisory / Non-polymer description
Revision 1.3Apr 9, 2014Group: Structure summary
Revision 1.4Aug 6, 2014Group: Structure summary
Revision 1.5Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2199
Polymers65,1081
Non-polymers2,1118
Water1,802100
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,43918
Polymers130,2162
Non-polymers4,22316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7030 Å2
ΔGint-53 kcal/mol
Surface area48420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.515, 102.166, 60.572
Angle α, β, γ (deg.)90.00, 114.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thioredoxin glutathione reductase


Mass: 65108.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: TGR / Plasmid: pCR2.1, pRSET A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: Q962Y6, EC: 1.6.4.5

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Non-polymers , 6 types, 108 molecules

#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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHOR STATES THAT THE RESIDUE 597 IS SEC (SELENOCYSTEINE). THERE IS X(UNK)597 IN SEQUENCE DATABASE.

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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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Hepes pH 7.0, 20% PEG3350, 0.1M KI, 5mM GSH, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 26954 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.7
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1329

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6o

2v6o


Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.516 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1346 5 %RANDOM
Rwork0.23014 ---
obs0.23145 25362 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.425 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20.68 Å2
2---2.64 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 103 100 4706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9131.9856423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6575601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14724.813187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67715810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3841518
X-RAY DIFFRACTIONr_chiral_restr0.0570.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023488
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1640.22088
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.23264
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2341.52932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43324737
X-RAY DIFFRACTIONr_scbond_it0.40631869
X-RAY DIFFRACTIONr_scangle_it0.6794.51681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 103 -
Rwork0.323 1846 -
obs--99.95 %

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