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

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Basic information

Entry
Database: PDB / ID: 6zlp
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 4-Aminopiazthiole
ComponentsThioredoxin glutathione reductase
KeywordsPROTEIN BINDING / secondary site / fragment binding / redox enzyme
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / 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 domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, dimerisation domain superfamily ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / 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. / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
2,1,3-benzothiadiazol-4-amine / FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFata, F. / Silvestri, I. / Williams, D.L. / Angelucci, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R33AI127635 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments.
Authors: Fata, F. / Silvestri, I. / Ardini, M. / Ippoliti, R. / Di Leandro, L. / Demitri, N. / Polentarutti, M. / Di Matteo, A. / Lyu, H. / Thatcher, G.R.J. / Petukhov, P.A. / Williams, D.L. / Angelucci, F.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)66,2416
Polymers65,1081
Non-polymers1,1335
Water6,269348
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,48212
Polymers130,2162
Non-polymers2,26610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1
Unit cell
Length a, b, c (Å)143.038, 101.807, 58.515
Angle α, β, γ (deg.)90.00, 112.95, 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, thioredoxin-disulfide reductase (NADPH)

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Non-polymers , 5 types, 353 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BTE / 2,1,3-benzothiadiazol-4-amine


Mass: 151.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 3350 20%, potassium iodide 0.2, BisTris 0.1M, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→39.8 Å / Num. obs: 41931 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3658 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6o

2v6o


Resolution: 2.15→37.003 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 2082 4.97 %
Rwork0.1786 --
obs0.1797 41923 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→37.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 72 348 4923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044671
X-RAY DIFFRACTIONf_angle_d0.6346339
X-RAY DIFFRACTIONf_dihedral_angle_d11.8422767
X-RAY DIFFRACTIONf_chiral_restr0.045721
X-RAY DIFFRACTIONf_plane_restr0.004799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.25461300.23812680X-RAY DIFFRACTION100
2.2-2.2550.25451550.23142639X-RAY DIFFRACTION100
2.255-2.3160.26291470.2172636X-RAY DIFFRACTION100
2.316-2.38411052648X-RAY DIFFRACTION100
2.3841-2.46110.24591340.20462651X-RAY DIFFRACTION100
2.4611-2.5490.20981540.20682640X-RAY DIFFRACTION100
2.549-2.65110.22391510.20412645X-RAY DIFFRACTION100
2.6511-2.77170.22391430.19532648X-RAY DIFFRACTION100
2.7717-2.91770.21181180.18552684X-RAY DIFFRACTION100
2.9177-3.10050.24291400.19232625X-RAY DIFFRACTION100
3.1005-3.33970.21781460.18252646X-RAY DIFFRACTION100
3.3397-3.67550.19841410.16392671X-RAY DIFFRACTION99
3.6755-4.20670.18031420.15312655X-RAY DIFFRACTION100
4.2067-5.29760.16331540.14142647X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.13030.4114-0.18112.9098-0.14821.6367-0.19380.39830.3343-0.88160.2828-0.6279-0.25980.2457-0.06510.5497-0.15990.13970.5013-0.07810.5489297.840421.865454.2037
22.55311.45030.93731.95450.63641.143-0.136-0.1798-0.2622-0.22170.1259-0.23520.0050.02190.00870.36710.03420.00520.3552-0.02060.3687280.5404-6.342161.2939
30.80480.0004-0.15831.4791-0.57980.9566-0.0937-0.3527-0.14390.17520.1034-0.0635-0.02490.0096-0.00890.3040.0528-0.00950.33680.00640.2138274.3822-6.911478.8348
41.63580.26590.34640.96701.0247-0.0717-0.18340.17640.05070.05930.0879-0.1672-0.1088-0.01520.30390.03390.00890.2404-0.04080.247266.275413.330165.3656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 396 )
4X-RAY DIFFRACTION4chain 'A' and (resid 397 through 593 )

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