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

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Basic information

Entry
Database: PDB / ID: 6zlb
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with Indole-3-carbinol
ComponentsThioredoxin glutathione reductase
KeywordsPROTEIN BINDING / secondary site / fragment binding / redox enzyme / inhibitor
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 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
FLAVIN-ADENINE DINUCLEOTIDE / 1~{H}-indol-3-ylmethanol / : / TRIETHYLENE GLYCOL / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)66,3477
Polymers65,1081
Non-polymers1,2396
Water10,106561
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,69514
Polymers130,2162
Non-polymers2,47812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area12230 Å2
ΔGint-65 kcal/mol
Surface area45910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.754, 101.830, 60.415
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1218-

HOH

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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

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Non-polymers , 6 types, 567 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-FXK / 1~{H}-indol-3-ylmethanol


Mass: 147.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 20%, potassium iodide 0.2M, bistris 0.1M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38 Å / Num. obs: 64412 / % possible obs: 99.1 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4009 / CC1/2: 0.775

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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: 1.9→37 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 3167 4.94 %
Rwork0.1683 --
obs0.1698 64098 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 80 561 5137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084686
X-RAY DIFFRACTIONf_angle_d0.8636353
X-RAY DIFFRACTIONf_dihedral_angle_d13.4252781
X-RAY DIFFRACTIONf_chiral_restr0.053721
X-RAY DIFFRACTIONf_plane_restr0.006799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-1.92850.29671450.25232527X-RAY DIFFRACTION95
1.9285-1.95870.26321470.2222624X-RAY DIFFRACTION99
1.9587-1.99080.26131360.21732628X-RAY DIFFRACTION99
1.9908-2.02510.23871320.21032660X-RAY DIFFRACTION99
2.0251-2.06190.2637950.19682645X-RAY DIFFRACTION99
2.0619-2.10160.24531460.18712635X-RAY DIFFRACTION99
2.1016-2.14450.22671360.17812651X-RAY DIFFRACTION99
2.1445-2.19110.20551550.17472639X-RAY DIFFRACTION99
2.1911-2.24210.20681690.17262611X-RAY DIFFRACTION99
2.2421-2.29810.19221340.15572639X-RAY DIFFRACTION100
2.2981-2.36030.20311060.16362724X-RAY DIFFRACTION99
2.3603-2.42970.2041430.15822625X-RAY DIFFRACTION99
2.4297-2.50810.23991310.17562664X-RAY DIFFRACTION100
2.5081-2.59770.24081620.17672620X-RAY DIFFRACTION100
2.5977-2.70170.21971290.17332666X-RAY DIFFRACTION100
2.7017-2.82470.20861450.16922675X-RAY DIFFRACTION99
2.8247-2.97350.20961200.16892664X-RAY DIFFRACTION99
2.9735-3.15980.1971290.16822688X-RAY DIFFRACTION99
3.1598-3.40360.20991410.16872659X-RAY DIFFRACTION100
3.4036-3.7460.17511290.15042670X-RAY DIFFRACTION99
3.746-4.28750.16221530.14172647X-RAY DIFFRACTION99
4.2875-5.39980.15611500.14172655X-RAY DIFFRACTION99
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)
10.93910.00690.07922.86291.71042.24850.01440.2997-0.2959-0.35910.1292-0.15310.20540.111-0.14060.3397-0.0419-0.00980.3278-0.050.3226-85.2216-26.6671-54.2243
22.74141.60841.14312.04120.96131.0391-0.0915-0.03390.0557-0.20060.0371-0.0125-0.1182-0.06830.06670.20230.01530.01230.18720.03010.23-79.13471.328-35.8504
30.7559-0.19750.05740.6738-0.05120.4134-0.0541-0.0922-0.04840.08320.07410.0797-0.0086-0.1018-0.0120.18440.00230.03470.19310.02910.2024-79.7696-9.3718-21.2322
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 592 )

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