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- PDB-6fp4: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 6fp4
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with 1,8-Naphthyridine-2-carboxylic acid
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
Chem-250 / 1,8-naphthyridine-2-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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 9, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)66,6597
Polymers65,1081
Non-polymers1,5516
Water1,63991
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,31914
Polymers130,2162
Non-polymers3,10312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area12640 Å2
ΔGint-69 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.316, 101.584, 58.783
Angle α, β, γ (deg.)90.00, 112.78, 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 BL21(DE3) (bacteria)
References: UniProt: G4V8J4, thioredoxin-disulfide reductase

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Non-polymers , 6 types, 97 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-E1T / 1,8-naphthyridine-2-carboxylic acid


Mass: 174.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-250 / (2R)-2-hydroxy-3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid


Mass: 268.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O5S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 59.12 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20%PEG 3350 0.1M bis-TRIS pH 7.0 0.2M KI 0.005M DTT

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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 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40.68 Å / Num. obs: 26602 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2937 / CC1/2: 0.753 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6O

2v6o


Resolution: 2.501→40.68 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.2292 1393 5.24 %
Rwork0.1953 --
obs0.1971 26580 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 104 91 4691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044697
X-RAY DIFFRACTIONf_angle_d0.6856364
X-RAY DIFFRACTIONf_dihedral_angle_d13.3472783
X-RAY DIFFRACTIONf_chiral_restr0.045720
X-RAY DIFFRACTIONf_plane_restr0.004796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5006-2.58990.3431310.30572446X-RAY DIFFRACTION97
2.5899-2.69360.29831570.26582480X-RAY DIFFRACTION100
2.6936-2.81620.29411400.25472528X-RAY DIFFRACTION100
2.8162-2.96460.29071100.25282550X-RAY DIFFRACTION100
2.9646-3.15030.31981380.24712512X-RAY DIFFRACTION100
3.1503-3.39340.25191330.21452538X-RAY DIFFRACTION100
3.3934-3.73470.22281350.19072523X-RAY DIFFRACTION100
3.7347-4.27460.19891450.16342510X-RAY DIFFRACTION99
4.2746-5.38360.19071680.14992520X-RAY DIFFRACTION100
5.3836-40.6850.19081360.17332580X-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)
11.16860.6054-0.15341.64690.00870.6936-0.07240.04590.063-0.17460.1346-0.2892-0.09520.2028-0.04820.4146-0.022-0.02180.4149-0.05190.4183145.7699.794261.2415
20.5611-0.15010.19031.3524-0.511.0728-0.1223-0.3852-0.02530.33820.1696-0.0804-0.09630.0245-0.04540.42870.0729-0.01210.4222-0.02840.3003128.0907-3.699481.7044
31.054-0.11960.29371.11290.06591.0174-0.1047-0.1280.16710.00560.09580.1307-0.1799-0.08030.00140.40240.0223-0.01020.3203-0.02250.3168120.168814.60163.9887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 307 )
2X-RAY DIFFRACTION2chain 'A' and (resid 308 through 415 )
3X-RAY DIFFRACTION3chain 'A' and (resid 416 through 592 )

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