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- PDB-6fmu: Thioredoxin glutathione reductase from Schistosome mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 6fmu
TitleThioredoxin glutathione reductase from Schistosome mansoni in complex with 2-[4-(4-amino-butyl)-piperazin-1-yl]-ethanol
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Fragment / Allosteric pocket / Schistosomiasis / FAD/NAD linked reductase
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 / Pyridine nucleotide-disulphide oxidoreductase, class I, active site ...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 / FAD/NAD-linked reductase, dimerisation domain superfamily / 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
2-[4-(4-azanylbutyl)piperazin-1-yl]ethanol / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSilvestri, I. / Fata, F. / MIele, A.E. / Boumis, G. / 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)1R21AI27635-01 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Fragment-Based Discovery of a Regulatory Site in Thioredoxin Glutathione Reductase Acting as "Doorstop" for NADPH Entry.
Authors: Silvestri, I. / Lyu, H. / Fata, F. / Boumis, G. / Miele, A.E. / Ardini, M. / Ippoliti, R. / Bellelli, A. / Jadhav, A. / Lea, W.A. / Simeonov, A. / Cheng, Q. / Arner, E.S.J. / Thatcher, G.R.J. ...Authors: Silvestri, I. / Lyu, H. / Fata, F. / Boumis, G. / Miele, A.E. / Ardini, M. / Ippoliti, R. / Bellelli, A. / Jadhav, A. / Lea, W.A. / Simeonov, A. / Cheng, Q. / Arner, E.S.J. / Thatcher, G.R.J. / Petukhov, P.A. / Williams, D.L. / Angelucci, F.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / 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 / _citation_author.name
Revision 1.2Mar 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 1.3Jan 17, 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)66,1984
Polymers65,0611
Non-polymers1,1373
Water9,962553
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3968
Polymers130,1222
Non-polymers2,2746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area10850 Å2
ΔGint-63 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.235, 102.257, 58.661
Angle α, β, γ (deg.)90.00, 112.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin glutathione reductase


Mass: 65061.145 Da / Num. of mol.: 1 / Mutation: U597C
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
#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-DVK / 2-[4-(4-azanylbutyl)piperazin-1-yl]ethanol


Mass: 201.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H23N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: Bis-tris 0.1M PH = 7.0; Peg 3350 20%; KI 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 71563 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7 / Num. unique obs: 4144 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6o

2v6o


Resolution: 1.8→37.13 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.1812 3516 4.91 %
Rwork0.1552 --
obs0.1565 71553 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 77 554 5134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014672
X-RAY DIFFRACTIONf_angle_d1.0816333
X-RAY DIFFRACTIONf_dihedral_angle_d12.7972778
X-RAY DIFFRACTIONf_chiral_restr0.059722
X-RAY DIFFRACTIONf_plane_restr0.007795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.8250.29251200.24092659X-RAY DIFFRACTION96
1.825-1.85110.23751260.20832677X-RAY DIFFRACTION99
1.8511-1.87870.23711290.19432727X-RAY DIFFRACTION99
1.8787-1.90810.23021400.1912703X-RAY DIFFRACTION99
1.9081-1.93930.23051500.18152711X-RAY DIFFRACTION99
1.9393-1.97280.20491320.17292710X-RAY DIFFRACTION99
1.9728-2.00860.20471340.17252682X-RAY DIFFRACTION99
2.0086-2.04730.21641320.17452747X-RAY DIFFRACTION100
2.0473-2.08910.23031530.172673X-RAY DIFFRACTION99
2.0891-2.13450.18431310.16842726X-RAY DIFFRACTION99
2.1345-2.18410.19431650.1552701X-RAY DIFFRACTION100
2.1841-2.23870.19551010.16062752X-RAY DIFFRACTION100
2.2387-2.29930.18641260.15262723X-RAY DIFFRACTION100
2.2993-2.36690.19741270.15392737X-RAY DIFFRACTION100
2.3669-2.44330.17581510.14752747X-RAY DIFFRACTION100
2.4433-2.53060.20141190.14992749X-RAY DIFFRACTION100
2.5306-2.63190.17591700.15342676X-RAY DIFFRACTION100
2.6319-2.75160.18581630.1512723X-RAY DIFFRACTION100
2.7516-2.89670.16811300.15142736X-RAY DIFFRACTION100
2.8967-3.07810.18481630.15512736X-RAY DIFFRACTION100
3.0781-3.31560.18921410.15452739X-RAY DIFFRACTION100
3.3156-3.6490.16911540.14442730X-RAY DIFFRACTION100
3.649-4.17640.13781440.13522743X-RAY DIFFRACTION100
4.1764-5.25940.13771450.12892751X-RAY DIFFRACTION100
5.2594-37.13760.19691700.17242779X-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)
10.09140.0024-0.07480.0384-0.05520.0589-0.0010.0520.0772-0.21520.0874-0.14050.0068-0.02240.00040.2759-0.07370.09450.2099-0.01040.3185156.849525.635351.5854
20.0499-0.02390.00970.04280.040.0572-0.0242-0.0656-0.0781-0.05480.0306-0.0524-0.01080.03-00.16450.0015-0.00240.17550.00240.1852135.6867-9.337661.6524
30.0179-0.02120.00260.034-0.01120.0076-0.0501-0.14190.04440.0420.0629-0.15970.07520.0942-00.1929-0.0185-0.02820.2482-0.04860.2709156.52136.731270.8275
40.3084-0.05960.0080.2194-0.07320.4056-0.0374-0.11030.02550.03350.0401-0.0043-0.0393-0.0146-00.15140.018-0.00210.1473-0.01290.1284125.13253.041571.5286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 218 )
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 261 )
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 593 )

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