+Open data
-Basic information
Entry | Database: PDB / ID: 3e0u | ||||||
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Title | Crystal structure of T. cruzi GPX1 | ||||||
Components | Glutathione peroxidase | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin fold / Peroxidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Patel, S.H. / Hussain, S. / Harris, R. / Driscoll, P. / Djordjevic, S. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Structural insights into the catalytic mechanism of Trypanosoma cruzi GPXI (glutathione peroxidase-like enzyme I). Authors: Patel, S. / Hussain, S. / Harris, R. / Sardiwal, S. / Kelly, J.M. / Wilkinson, S.R. / Driscoll, P.C. / Djordjevic, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e0u.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e0u.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0u ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0u | HTTPS FTP |
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-Related structure data
Related structure data | 2p5rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18282.977 Da / Num. of mol.: 1 / Fragment: UNP residues 14 to 177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: GPXI / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: Q8T8E2, glutathione peroxidase | ||
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#2: Chemical | ChemComp-NH4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.9 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.47 Å / Num. all: 7987 / Num. obs: 7515 / % possible obs: 94.1 % |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on 2P5R, all loops deleted Resolution: 2.3→25.42 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.762 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.256 / 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: 49.509 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.8636 Å / Origin y: 0.6712 Å / Origin z: 10.2885 Å
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