+Open data
-Basic information
Entry | Database: PDB / ID: 3tue | ||||||
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Title | The structure of tryparedoxin peroxidase I from Leishmania major | ||||||
Components | Tryparedoxin peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Thioredoxin fold / peroxidase / peroxiredoxin | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / peroxiredoxin activity / cell redox homeostasis / hydrogen peroxide catabolic process / cilium / response to oxidative stress / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Fiorillo, A. / Ilari, A. / Colotti, G. | ||||||
Citation | Journal: Plos Negl Trop Dis / Year: 2012 Title: The crystal structures of the tryparedoxin-tryparedoxin peroxidase couple unveil the structural determinants of leishmania detoxification pathway. Authors: Fiorillo, A. / Colotti, G. / Boffi, A. / Baiocco, P. / Ilari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tue.cif.gz | 171.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tue.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/3tue ftp://data.pdbj.org/pub/pdb/validation_reports/tu/3tue | HTTPS FTP |
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-Related structure data
Related structure data | 3s9fC 1e2yS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24332.775 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: TRYP3, LMJF_15_1080 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QF76, peroxiredoxin #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22% PEG 3350, 0.1 M BIS-TRIS PROPANE, 0.2 M KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2011 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 3→106 Å / Num. obs: 21162 / % possible obs: 99.9 % / Redundancy: 2.9 % / Rsym value: 0.15 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.84 / Rsym value: 0.518 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E2Y Resolution: 3→106 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU B: 14.645 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 36.861 Å2
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Refinement step | Cycle: LAST / Resolution: 3→106 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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