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Yorodumi- PDB-3t59: C76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t59 | ||||||
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Title | C76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide | ||||||
Components | Sulfhydryl oxidase 1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation / FAD binding / protein folding / Golgi membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Fass, D. / Alon, A. / Gat, Y. | ||||||
Citation | Journal: Nature / Year: 2012 Title: The dynamic disulphide relay of quiescin sulphydryl oxidase. Authors: Alon, A. / Grossman, I. / Gat, Y. / Kodali, V.K. / DiMaio, F. / Mehlman, T. / Haran, G. / Baker, D. / Thorpe, C. / Fass, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t59.cif.gz | 403 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t59.ent.gz | 339.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t59_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3t59_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3t59_validation.xml.gz | 84.6 KB | Display | |
Data in CIF | 3t59_validation.cif.gz | 113.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t59 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t59 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 58101.789 Da / Num. of mol.: 4 / Fragment: UNP residues 36-550 / Mutation: C76A, C455S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qscn6, Qsox1, QSOX1b, Sox / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q8BND5, thiol oxidase #2: Chemical | ChemComp-FAD / #3: 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: 2.87 Å3/Da / Density % sol: 57.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1M HEPES pH 7.0, 10% 1,5 pentadiol, 5% glycerol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 16, 2011 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 64397 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 15.362 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.514 / Rsym value: 0.266 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Resolution: 2.8→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 34
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Solvent computation | Bsol: 35.3371 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.8136 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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