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Yorodumi- PDB-6mws: crystal structure of the reduced Grx1 from Saccharomyces cerevisiae -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mws | ||||||
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Title | crystal structure of the reduced Grx1 from Saccharomyces cerevisiae | ||||||
Components | Glutaredoxin-1 | ||||||
Keywords | OXIDOREDUCTASE / Glutaredoxin 1 / yeast Saccharomyces cerevisiae | ||||||
Function / homology | Function and homology information glutathione peroxidase / glutathione disulfide oxidoreductase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / cellular response to oxidative stress / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å | ||||||
Authors | Maghool, S. / Maher, J.M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: High-resolution crystal structure of the reduced Grx1 from Saccharomyces cerevisiae. Authors: Maghool, S. / La Fontaine, S. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mws.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mws.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 6mws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/6mws ftp://data.pdbj.org/pub/pdb/validation_reports/mw/6mws | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12805.607 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: GRX1, YCL035C, YCL35C / Production host: Escherichia coli (E. coli) / References: UniProt: P25373 |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.23 M Lithium sulfate monohydrate, 0.1 M Bis-Tris, pH 5.8, 26% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953654 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953654 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→41.36 Å / Num. obs: 37323 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.056 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.22→1.24 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.319 / Num. unique obs: 1777 / CC1/2: 0.969 / Rpim(I) all: 0.107 / Rrim(I) all: 0.337 / % possible all: 98.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→38.38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.727 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.035 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.86 Å2 / Biso mean: 13.895 Å2 / Biso min: 7.78 Å2
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Refinement step | Cycle: final / Resolution: 1.22→38.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.251 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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