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Yorodumi- PDB-4dsr: Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dsr | ||||||
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Title | Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in reduced form | ||||||
Components | Peroxiredoxin type-2 | ||||||
Keywords | OXIDOREDUCTASE / PEROXIREDOXIN / Peroxidase / Thioredoxin-like Fold / Alkyl hydroperoxide reductase | ||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion ...TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Lian, F.M. / Yu, J. / Ma, X.X. / Yu, X.J. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Snapshots of Yeast Alkyl Hydroperoxide Reductase Ahp1 Peroxiredoxin Reveal a Novel Two-cysteine Mechanism of Electron Transfer to Eliminate Reactive Oxygen Species. Authors: Lian, F.M. / Yu, J. / Ma, X.X. / Yu, X.J. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dsr.cif.gz | 138 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dsr.ent.gz | 109.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dsr_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 4dsr_full_validation.pdf.gz | 466.7 KB | Display | |
Data in XML | 4dsr_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 4dsr_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/4dsr ftp://data.pdbj.org/pub/pdb/validation_reports/ds/4dsr | HTTPS FTP |
-Related structure data
Related structure data | 4dsqC 4dssC 1tp9S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20149.730 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288C / Gene: AHP1, L2916, L9354.5, YLR109W / Plasmid: pET28a-derived / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P38013, peroxiredoxin #2: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% polyethylene glycol 3350, 0.2M ammonium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→50 Å / Num. all: 16465 / Num. obs: 16465 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 70.2 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 7.68 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.991 / Num. unique all: 1642 / Rsym value: 0.369 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TP9 Resolution: 2.91→44.2 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R Free: 0.494 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→44.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.91→2.986 Å / Total num. of bins used: 20
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