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

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Basic information

Entry
Database: PDB / ID: 6rtm
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 1-[(dimethylamino)methyl]-2-naphthol at 2 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


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding / electron transfer activity
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 / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / 1-methylidenenaphthalen-2-one / TRIETHYLENE GLYCOL / thioredoxin-disulfide reductase / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Assembly

Deposited unit
A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3896
Polymers65,1081
Non-polymers1,2815
Water5,711317
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,77812
Polymers130,2162
Non-polymers2,56210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area11920 Å2
ΔGint-56 kcal/mol
Surface area46250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.042, 102.002, 58.540
Angle α, β, γ (deg.)90.000, 112.780, 90.000
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 , 5 types, 322 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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-KJH / 1-methylidenenaphthalen-2-one


Mass: 156.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, 0.2M KI, 0.1 Mi BISTRIS, 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: 2.1→40.5 Å / Num. obs: 44319 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.627 / Num. unique obs: 3577

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6o

2v6o


Resolution: 2.1→40.5 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.39
RfactorNum. reflection% reflection
Rfree0.2344 2183 4.93 %
Rwork0.1835 --
obs0.1858 44285 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.21 Å2 / Biso mean: 48.6999 Å2 / Biso min: 18.75 Å2
Refinement stepCycle: final / Resolution: 2.1→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 153 317 4969
Biso mean--52.31 43.14 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124681
X-RAY DIFFRACTIONf_angle_d1.156347
X-RAY DIFFRACTIONf_chiral_restr0.062721
X-RAY DIFFRACTIONf_plane_restr0.008796
X-RAY DIFFRACTIONf_dihedral_angle_d13.4042780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.14450.32261500.2549256097
2.1445-2.19440.2736149257298
2.1944-2.24930.3215153261598
2.2493-2.31010.3298148257698
2.3101-2.37810.2675135261898
2.3781-2.45480.2514121265998
2.4548-2.54250.2645164258598
2.5425-2.64430.2586136260599
2.6443-2.76460.25731270.1854264799
2.7646-2.91030.21321230.1851264499
2.9103-3.09260.2293134263098
3.0926-3.33130.24521270.1867262799
3.3313-3.66640.24661110.1764270799
3.6664-4.19640.21131430.156266499
4.1964-5.28520.19091280.1524267199
5.2852-100.20111340.181272299

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