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Open data
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Basic information
Entry | Database: PDB / ID: 6krm | |||||||||
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Title | Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F46A mutant | |||||||||
![]() | Peroxiredoxin | |||||||||
![]() | OXIDOREDUCTASE / Peroxiredoxin | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Himiyama, T. / Nakamura, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Disassembly of the ring-type decameric structure of peroxiredoxin from Aeropyrum pernix K1 by amino acid mutation. Authors: Himiyama, T. / Nakamura, 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 | ![]() | 528.4 KB | Display | ![]() |
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PDB format | ![]() | 421.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 536.4 KB | Display | ![]() |
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Full document | ![]() | 581.1 KB | Display | |
Data in XML | ![]() | 104.7 KB | Display | |
Data in CIF | ![]() | 144.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6krkC ![]() 6krpC ![]() 6krqC ![]() 6krrC ![]() 6krsC ![]() 2e2gS 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: 28619.734 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 263527 / % possible obs: 97 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12878 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E2G Resolution: 1.8→49.252 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.585 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.939 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.252 Å
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Refine LS restraints |
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LS refinement shell |
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