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Yorodumi- PDB-5dky: Crystal structure of glucosidase II alpha subunit (DNJ-bound from) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dky | |||||||||
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Title | Crystal structure of glucosidase II alpha subunit (DNJ-bound from) | |||||||||
Components | Alpha glucosidase-like protein | |||||||||
Keywords | HYDROLASE / ENDOPLASMIC RETICULUM / GLYCOSIDE HYDROLASE / GLYCOSYLATION | |||||||||
Function / homology | Function and homology information alpha-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | |||||||||
Authors | Satoh, T. / Toshimori, T. / Yan, G. / Yamaguchi, T. / Kato, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control. Authors: Satoh, T. / Toshimori, T. / Yan, G. / Yamaguchi, T. / Kato, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dky.cif.gz | 219.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dky.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/5dky ftp://data.pdbj.org/pub/pdb/validation_reports/dk/5dky | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 108501.156 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-977 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0064960 / Plasmid: pCold-GST (modified) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G0SG42 |
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#2: Chemical | ChemComp-NOJ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 M sodium citrate tribasic, 0.1 M Tris-HCl (pH 7.0), 2.5 mM DNJ |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 141836 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.8 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.482 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / 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: 20.444 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→20 Å
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Refine LS restraints |
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