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Yorodumi- PDB-5w1l: Echinococcus granulosus thioredoxin glutathione reductas (egTGR) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w1l | ||||||
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Title | Echinococcus granulosus thioredoxin glutathione reductas (egTGR) with Gold | ||||||
Components | (Thioredoxin glutathione reductase) x 2 | ||||||
Keywords | SIGNALING PROTEIN / egTGR / redox / antioxidant | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Echinococcus granulosus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.88 Å | ||||||
Authors | Gao, W. / Wang, Y. / Dai, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w1l.cif.gz | 468.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w1l.ent.gz | 395.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w1l ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w1l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | ||
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#2: Protein | 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 | #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.99 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→100 Å / Num. obs: 36052 / % possible obs: 99 % / Redundancy: 13.2 % / Net I/σ(I): 16.8 |
-Processing
Software |
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Refinement | Resolution: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.281 Å2
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Refinement step | Cycle: 1 / Resolution: 2.88→100.72 Å
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Refine LS restraints |
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