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- PDB-7cqj: Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/K84A/C207S/C2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cqj | |||||||||
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Title | Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/K84A/C207S/C213S mutant (ApPrx*K84A) | |||||||||
![]() | 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: Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification. Authors: Himiyama, T. / Tsuchiya, Y. / Yonezawa, Y. / 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 | ![]() | 587 KB | Display | ![]() |
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PDB format | ![]() | 474.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 522.7 KB | Display | ![]() |
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Full document | ![]() | 569.6 KB | Display | |
Data in XML | ![]() | 96 KB | Display | |
Data in CIF | ![]() | 131 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c87C ![]() 7c89C ![]() 7c8aC ![]() 6krkS S: Starting model for refinement C: citing same article ( |
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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: 28637.727 Da / Num. of mol.: 12 / Mutation: C50S,K84A,C207S,C213S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9Y9L0, thioredoxin-dependent peroxiredoxin #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: The reservoir solution contained 0.10 M sodium acetate trihydrate (pH 4.6) 0.20 M calcium chloride dihydrate 20 %v/v 2-propanol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.48 Å / Num. obs: 83831 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.9→2.96 Å / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4559 / CC1/2: 0.763 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6krk Resolution: 2.9→49.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 16.753 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.418 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→49.48 Å
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Refine LS restraints |
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LS refinement shell |
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