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- PDB-2e2m: Crystal structure of archaeal peroxiredoxin, thioredoxin peroxida... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2e2m | ||||||
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Title | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form) | ||||||
![]() | Probable peroxiredoxin | ||||||
![]() | OXIDOREDUCTASE / cysteine sulfenic acid / cysteine sulfinic acid / cysteine sulfonic acid / hypervalent sulfur compound / peroxidatic cysteine | ||||||
Function / homology | ![]() thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T. | ||||||
![]() | ![]() Title: Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate Authors: Nakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 466.5 KB | Display | ![]() |
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PDB format | ![]() | 387 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 513.1 KB | Display | ![]() |
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Full document | ![]() | 535 KB | Display | |
Data in XML | ![]() | 83.3 KB | Display | |
Data in CIF | ![]() | 112.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e2gC ![]() 2nvlC ![]() 2zctC ![]() 1x0rS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28759.957 Da / Num. of mol.: 10 / Mutation: C207S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M sodium acetate pH4.8, 0.2M calcium chloride, 10%(v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 80972 / % possible obs: 94.5 % |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 77.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X0R Resolution: 2.6→39.37 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.858 / SU B: 14.18 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.813 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→39.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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