[English] 日本語
Yorodumi- PDB-2e2g: Crystal structure of archaeal peroxiredoxin, thioredoxin peroxida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e2g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form) | ||||||
Components | Probable peroxiredoxin | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin peroxidase / cysteine sulfenic acid / cysteine sulfinic acid / cysteine sulfonic acid / hypervalent sulfur compound / peroxidatic cysteine | ||||||
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: 2.4 Å | ||||||
Authors | Nakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate Authors: Nakamura, T. / Yamamoto, T. / Abe, M. / Matsumura, H. / Hagihara, Y. / Goto, T. / Yamaguchi, T. / Inoue, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2e2g.cif.gz | 476.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2e2g.ent.gz | 395.1 KB | Display | PDB format |
PDBx/mmJSON format | 2e2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/2e2g ftp://data.pdbj.org/pub/pdb/validation_reports/e2/2e2g | HTTPS FTP |
---|
-Related structure data
Related structure data | 2e2mC 2nvlC 2zctC 1x0rS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28727.957 Da / Num. of mol.: 10 / Mutation: C207S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9Y9L0, peroxiredoxin #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M Acetate buffer pH4.8, 0.2M calcium chloride, 10%(v/v)isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 115754 / % possible obs: 87.2 % / Redundancy: 2.4 % |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 71.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X0R Resolution: 2.4→19.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.413 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.484 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.452 Å / Total num. of bins used: 20
|