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Yorodumi- PDB-5y4u: Crystal structure of Grx domain of Grx3 from Saccharomyces cerevisiae -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y4u | |||||||||
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Title | Crystal structure of Grx domain of Grx3 from Saccharomyces cerevisiae | |||||||||
Components | Monothiol glutaredoxin-3 | |||||||||
Keywords | OXIDOREDUCTASE / monothiol glutaredoxin / glutathione | |||||||||
Function / homology | Function and homology information negative regulation of transcription regulatory region DNA binding / disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / actin cytoskeleton organization / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / metal ion binding ...negative regulation of transcription regulatory region DNA binding / disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / actin cytoskeleton organization / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Chi, C.B. / Tang, Y.J. / Zhang, J.H. / Dai, Y.N. / Abdalla, M. / Chen, Y.X. / Zhou, C.Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2018 Title: Structural and Biochemical Insights into the Multiple Functions of Yeast Grx3. Authors: Chi, C.B. / Tang, Y. / Zhang, J. / Dai, Y.N. / Abdalla, M. / 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 | 5y4u.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y4u.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 5y4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/5y4u ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y4u | HTTPS FTP |
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-Related structure data
Related structure data | 5y4bC 5y4tC 3zywS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 13441.141 Da / Num. of mol.: 1 / Fragment: UNP residues 144-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: GRX3, YDR098C, YD8557.05C / Production host: Escherichia coli (E. coli) / References: UniProt: Q03835 |
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#2: 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: 1.61 Å3/Da / Density % sol: 23.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl, pH 8.0, 2 M Ammonium sulfate / PH range: 7.8 - 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.5418 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 10493 / % possible obs: 97 % / Redundancy: 4.2 % / Net I/σ(I): 20.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZYW Resolution: 1.7→25.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.689 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.123 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.346 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→25.46 Å
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Refine LS restraints |
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