+Open data
-Basic information
Entry | Database: PDB / ID: 6krs | |||||||||
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Title | Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W211A mutant | |||||||||
Components | Peroxiredoxin | |||||||||
Keywords | OXIDOREDUCTASE / Peroxiredoxin | |||||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / antioxidant activity / cellular response to hydrogen peroxide / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Aeropyrum pernix (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Himiyama, T. / Nakamura, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Protein Sci. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6krs.cif.gz | 478.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6krs.ent.gz | 398.2 KB | Display | PDB format |
PDBx/mmJSON format | 6krs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6krs ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6krs | HTTPS FTP |
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-Related structure data
Related structure data | 6krkC 6krmC 6krpC 6krqC 6krrC 2e2gS 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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-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.) Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (archaea) Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1 Gene: APE_2278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y9L0, peroxiredoxin #2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.71 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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