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Open data
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Basic information
Entry | Database: PDB / ID: 6krs | |||||||||
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Title | Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W211A 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 | ![]() | 478.4 KB | Display | ![]() |
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PDB format | ![]() | 398.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 533.6 KB | Display | ![]() |
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Full document | ![]() | 570.3 KB | Display | |
Data in XML | ![]() | 88.2 KB | Display | |
Data in CIF | ![]() | 117.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6krkC ![]() 6krmC ![]() 6krpC ![]() 6krqC ![]() 6krrC ![]() 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: 27647.592 Da / Num. of mol.: 10 / Mutation: C50S, W211A, C207S, C213S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1 Gene: APE_2278 / Production host: ![]() ![]() #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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 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: Jul 14, 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: 2.3→50 Å / Num. obs: 130548 / % possible obs: 97.9 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.059 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 6421 / CC1/2: 0.982 / Rrim(I) all: 0.295 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E2G Resolution: 2.3→49.363 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→49.363 Å
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LS refinement shell | Resolution: 2.3→2.36 Å /
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