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Yorodumi- PDB-5ykw: Structural basis of the thiol resolving mechanism in yeast mitoch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ykw | ||||||
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Title | Structural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems | ||||||
Components |
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Keywords | TRANSFERASE / Saccharomyces cerevisiae / 1-Cys Peroxiredoxin / Thioredoxin / glutathione | ||||||
Function / homology | Function and homology information : / glutaredoxin-dependent peroxiredoxin / glutathione-dependent peroxiredoxin / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / thioredoxin peroxidase activity / Oxidative Stress Induced Senescence ...: / glutaredoxin-dependent peroxiredoxin / glutathione-dependent peroxiredoxin / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / thioredoxin peroxidase activity / Oxidative Stress Induced Senescence / response to cadmium ion / Neutrophil degranulation / cell redox homeostasis / peroxidase activity / cellular response to oxidative stress / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 Å | ||||||
Authors | Li, C.C. / Yang, J. / Yang, M.J. / Liu, L. / Peng, C.T. / Li, T. / He, L.H. / Song, Y.J. / Zhu, Y.B. / Zhao, N.L. ...Li, C.C. / Yang, J. / Yang, M.J. / Liu, L. / Peng, C.T. / Li, T. / He, L.H. / Song, Y.J. / Zhu, Y.B. / Zhao, N.L. / Zhao, C. / Bao, R. | ||||||
Citation | Journal: to be published Title: Structural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems Authors: Li, C.C. / Yang, J. / Yang, M.J. / Liu, L. / Peng, C.T. / Li, T. / He, L.H. / Song, Y.J. / Zhu, Y.B. / Zhao, N.L. / Zhao, C. / Bao, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ykw.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ykw.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ykw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ykw_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 5ykw_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 5ykw_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 5ykw_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5ykw ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5ykw | HTTPS FTP |
-Related 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: 11835.740 Da / Num. of mol.: 1 / Mutation: C35S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TRX3, YCR083W, YCR83W / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25372 |
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#2: Protein/peptide | Mass: 848.960 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: PRX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34227*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% (W/V) PEG-2000 MME ,100mM Tris base/Hydrochloric acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.075→40 Å / Num. obs: 8273 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rsym value: 0.161 / Net I/σ(I): 7.43 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.22 / Rsym value: 0.555 / % possible all: 92.9 |
-Processing
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Refinement | Resolution: 2.08→32.65 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 21.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→32.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.4152 Å / Origin y: 55.0273 Å / Origin z: -6.2755 Å
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Refinement TLS group | Selection details: ALL |