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- PDB-5w1l: Echinococcus granulosus thioredoxin glutathione reductas (egTGR) ... -

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Basic information

Entry
Database: PDB / ID: 5w1l
TitleEchinococcus granulosus thioredoxin glutathione reductas (egTGR) with Gold
Components(Thioredoxin glutathione reductase) x 2
KeywordsSIGNALING PROTEIN / egTGR / redox / antioxidant
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / : / Glutaredoxin domain profile. / 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 ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / : / Glutaredoxin domain profile. / 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 / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / thioredoxin-disulfide reductase (NADPH)
Similarity search - Component
Biological speciesEchinococcus granulosus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.88 Å
AuthorsGao, W. / Wang, Y. / Dai, S.
CitationJournal: Antioxid. Redox Signal. / Year: 2017
Title: The Enzymatic and Structural Basis for Inhibition of Echinococcus granulosus Thioredoxin Glutathione Reductase by Gold(I).
Authors: Salinas, G. / Gao, W. / Wang, Y. / Bonilla, M. / Yu, L. / Novikov, A. / Virginio, V.G. / Ferreira, H.B. / Vieites, M. / Gladyshev, V.N. / Gambino, D. / Dai, S.
History
DepositionJun 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin glutathione reductase
B: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8726
Polymers128,9072
Non-polymers1,9654
Water00
1
A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5473
Polymers64,5641
Non-polymers9832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3253
Polymers64,3431
Non-polymers9832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.346, 109.346, 258.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin glutathione reductase


Mass: 64564.031 Da / Num. of mol.: 1 / Fragment: UNP residues 34-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinococcus granulosus (invertebrata) / Gene: TGR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q869D7
#2: Protein Thioredoxin glutathione reductase


Mass: 64342.918 Da / Num. of mol.: 1 / Fragment: UNP residues 34-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinococcus granulosus (invertebrata) / Gene: TGR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q869D7
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) polyethylene glycol 3350, 0.1 M lithium sulfate, 0.1 M Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.87→100 Å / Num. obs: 36052 / % possible obs: 99 % / Redundancy: 13.2 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.88→100.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.909 / SU B: 38.771 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24898 1804 5 %RANDOM
Rwork0.18465 ---
obs0.18786 34270 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.88→100.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 108 0 9114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199324
X-RAY DIFFRACTIONr_bond_other_d0.0020.028490
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.96712665
X-RAY DIFFRACTIONr_angle_other_deg1.2319735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.74751166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47624.621409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.161151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0561544
X-RAY DIFFRACTIONr_chiral_restr0.1230.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110376
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021850
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0724.0374673
X-RAY DIFFRACTIONr_mcbond_other2.0724.0374672
X-RAY DIFFRACTIONr_mcangle_it3.4056.0565836
X-RAY DIFFRACTIONr_mcangle_other3.4056.0565837
X-RAY DIFFRACTIONr_scbond_it2.2314.2534651
X-RAY DIFFRACTIONr_scbond_other2.2314.2534652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6166.2896830
X-RAY DIFFRACTIONr_long_range_B_refined5.57647.69810472
X-RAY DIFFRACTIONr_long_range_B_other5.57547.69610473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.879→2.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 135 -
Rwork0.327 2482 -
obs--99.2 %
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)
11.4295-0.0641-0.26611.1225-0.00911.6387-0.0348-0.08390.03240.15660.04890.05010.20080.0318-0.0140.29020.0903-0.00420.27230.0320.0087-5.5293-38.58920.3541
21.53730.1762-0.18111.3210.38082.2916-0.0520.1590.0481-0.10460.1093-0.15620.11040.2966-0.05730.21350.0294-0.00990.4295-0.05780.030213.9412-39.4339-13.7787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 602
2X-RAY DIFFRACTION2B4 - 602

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