+Open data
-Basic information
Entry | Database: PDB / ID: 6iu1 | ||||||
---|---|---|---|---|---|---|---|
Title | Peroxiredoxin from Pyrococcus horikoshii 0Cys mutant) | ||||||
Components | Peroxiredoxin | ||||||
Keywords | OXIDOREDUCTASE / hydrogen peroxide / decamer | ||||||
Function / homology | Function and homology information cellular response to stress / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / cellular response to oxygen levels / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Nakamura, T. / Himiyama, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: J.Biochem. / Year: 2019 Title: Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis. Authors: Himiyama, T. / Oshima, M. / Uegaki, K. / Nakamura, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6iu1.cif.gz | 816.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6iu1.ent.gz | 682.6 KB | Display | PDB format |
PDBx/mmJSON format | 6iu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iu1_validation.pdf.gz | 603.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6iu1_full_validation.pdf.gz | 703.8 KB | Display | |
Data in XML | 6iu1_validation.xml.gz | 145.3 KB | Display | |
Data in CIF | 6iu1_validation.cif.gz | 198.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/6iu1 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/6iu1 | HTTPS FTP |
-Related structure data
Related structure data | 6itzC 6iu0C 3w6gS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24742.502 Da / Num. of mol.: 20 / Mutation: C46S,C205S,C211S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Production host: Escherichia coli (E. coli) / References: UniProt: O58966, peroxiredoxin #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES-NaOH (pH 7.5), 0.2M NaCl, and 20% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→40 Å / Num. obs: 111510 / % possible obs: 98.7 % / Redundancy: 6.6 % / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.9→2.95 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W6G Resolution: 2.89→39.09 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.848 / SU B: 21.163 / SU ML: 0.394 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.534 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.89→39.09 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|