+Open data
-Basic information
Entry | Database: PDB / ID: 3l4n | ||||||
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Title | Crystal structure of yeast monothiol glutaredoxin Grx6 | ||||||
Components | Monothiol glutaredoxin-6 | ||||||
Keywords | OXIDOREDUCTASE / C-terminal domain of Grx6 | ||||||
Function / homology | Function and homology information glutathione-disulfide reductase (NADPH) activity / glutathione disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / fungal-type vacuole / cis-Golgi network / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / Golgi lumen / cellular response to oxidative stress / intracellular iron ion homeostasis ...glutathione-disulfide reductase (NADPH) activity / glutathione disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / fungal-type vacuole / cis-Golgi network / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / Golgi lumen / cellular response to oxidative stress / intracellular iron ion homeostasis / iron ion binding / endoplasmic reticulum membrane / Golgi apparatus / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Luo, M. / Jiang, Y.-L. / Ma, X.-X. / He, Y.-X. / Tang, Y.-J. / Yu, J. / Zhang, R.-G. / Chen, Y. / Zhou, C.-Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural and biochemical characterization of yeast monothiol glutaredoxin Grx6 Authors: Luo, M. / Jiang, Y.-L. / Ma, X.-X. / Tang, Y.-J. / He, Y.-X. / Yu, J. / Zhang, R.-G. / 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 | 3l4n.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l4n.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 3l4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4n ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4n | 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: 14754.483 Da / Num. of mol.: 1 / Fragment: Grx6 C-terminal Grx domain, UNP residues 113-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: GRX6, YDL010W, D2890 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) References: UniProt: Q12438, glutathione-disulfide reductase |
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#2: Chemical | ChemComp-GSH / |
#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: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 19% polyethylene glycol monomethyl ether 5000, 0.1M 2-(N-morpholino)-ethane sulfonic acid (MES), pH 6.5, 10mM reduced glutathione (GSH), VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2008 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 27154 / % possible obs: 96.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 35.13 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.26 / Num. unique all: 1301 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→25.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.31 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.064 / 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: 18.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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