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Yorodumi- PDB-4owy: Crystal Structure of Ahp1 from Saccharomyces cerevisiae. Investig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4owy | ||||||
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Title | Crystal Structure of Ahp1 from Saccharomyces cerevisiae. Investigating the electron transfers. | ||||||
Components | Peroxiredoxin type-2 | ||||||
Keywords | OXIDOREDUCTASE / Peroxiredoxin / Ahp1 / Electron Transfer | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Schultz, L. / Genu, V. / Breyer, C.A. / dos Santos, V.F. / Guimaraes, B.G. / Netto, L.E.S. / de Oliveira, M.A. | ||||||
Citation | Journal: To be published Title: Crystal Structure of Ahp1 from Saccharomyces cerevisiae. Investigating the electron transfers. Authors: Schultz, L. / Genu, V. / Breyer, C.A. / dos Santos, V.F. / Guimaraes, B.G. / de Oliveira, M.A. / Netto, L.E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4owy.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4owy.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 4owy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/4owy ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4owy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 21303.971 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: BY4741 / Gene: AHP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P38013, peroxiredoxin #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-TBU / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.13 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3000, 0.2M CaAc and 0.1M Bis-Tris Propane |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2007 |
Radiation | Monochromator: Single Crystal Monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.421 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.64 Å / Num. obs: 32233 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.416 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→42.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.593 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→42.6 Å
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Refine LS restraints |
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