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- PDB-6rtj: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 6rtj
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 1-[(dimethylamino)methyl]-2-naphthol at 1 hour of soaking
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Fragment / secondary site / Schistosomiasis / FAD/NAD linked reductase / time-resolved structural studies
Function / homology
Function and homology information


glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / glutathione metabolic process / cell redox homeostasis / cellular response to oxidative stress / flavin adenine dinucleotide binding / electron transfer activity / mitochondrion ...glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / glutathione metabolic process / cell redox homeostasis / cellular response to oxidative stress / flavin adenine dinucleotide binding / electron transfer activity / 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 / 1-[(dimethylamino)methyl]naphthalen-2-ol / TRIETHYLENE GLYCOL / thioredoxin-disulfide reductase / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAngelucci, F. / Silvestri, I. / Fata, F. / Williams, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33AI127635 United States
CitationJournal: Free Radic Biol Med / Year: 2020
Title: Ectopic suicide inhibition of thioredoxin glutathione reductase.
Authors: Silvestri, I. / Lyu, H. / Fata, F. / Banta, P.R. / Mattei, B. / Ippoliti, R. / Bellelli, A. / Pitari, G. / Ardini, M. / Petukhova, V. / Thatcher, G.R.J. / Petukhov, P.A. / Williams, D.L. / Angelucci, F.
History
DepositionMay 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)66,4796
Polymers65,1081
Non-polymers1,3715
Water6,089338
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,95912
Polymers130,2162
Non-polymers2,74310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11780 Å2
ΔGint-84 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.665, 102.187, 58.521
Angle α, β, γ (deg.)90.00, 112.89, 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: Smp_048430 / Production host: Escherichia coli (E. coli)
References: UniProt: G4V8J4, UniProt: A0A3Q0KFL1*PLUS, thioredoxin-disulfide reductase

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Non-polymers , 6 types, 343 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-FXH / 1-[(dimethylamino)methyl]naphthalen-2-ol


Mass: 201.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, BISTRIS 0.1M pH 7.0, 0.2M KI, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.79 Å / Num. obs: 51649 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.639 / Num. unique obs: 3788

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6o

2v6o


Resolution: 2→39.79 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2
RfactorNum. reflection% reflection
Rfree0.2235 2619 5.07 %
Rwork0.1841 --
obs0.1861 51628 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 92 338 4933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124698
X-RAY DIFFRACTIONf_angle_d1.1466369
X-RAY DIFFRACTIONf_dihedral_angle_d18.3041722
X-RAY DIFFRACTIONf_chiral_restr0.063722
X-RAY DIFFRACTIONf_plane_restr0.008800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03640.28011420.25562562X-RAY DIFFRACTION99
2.0364-2.07550.30821320.23952545X-RAY DIFFRACTION99
2.0755-2.11790.30281210.23272552X-RAY DIFFRACTION98
2.1179-2.1640.22871260.2192616X-RAY DIFFRACTION99
2.164-2.21430.29921510.2132523X-RAY DIFFRACTION99
2.2143-2.26970.25341440.19922578X-RAY DIFFRACTION99
2.2697-2.3310.23871550.19592539X-RAY DIFFRACTION99
2.331-2.39960.27571410.19272572X-RAY DIFFRACTION99
2.3996-2.4770.25051230.19842584X-RAY DIFFRACTION99
2.477-2.56560.2575990.20292630X-RAY DIFFRACTION99
2.5656-2.66830.25631340.19272598X-RAY DIFFRACTION99
2.6683-2.78970.22421500.19682587X-RAY DIFFRACTION99
2.7897-2.93670.27681280.19832592X-RAY DIFFRACTION99
2.9367-3.12060.2331650.19992539X-RAY DIFFRACTION99
3.1206-3.36150.20241520.17812574X-RAY DIFFRACTION99
3.3615-3.69950.21021280.16462619X-RAY DIFFRACTION99
3.6995-4.23430.19831240.15332600X-RAY DIFFRACTION99
4.2343-5.33280.17651620.15142571X-RAY DIFFRACTION99
5.3328-39.80270.2041420.18762628X-RAY DIFFRACTION98

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