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Yorodumi- PDB-5dkx: Crystal structure of glucosidase II alpha subunit (Tris-bound from) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dkx | |||||||||
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Title | Crystal structure of glucosidase II alpha subunit (Tris-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: 1.4 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 | 5dkx.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dkx.ent.gz | 178.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/5dkx ftp://data.pdbj.org/pub/pdb/validation_reports/dk/5dkx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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-TRS / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.7 M sodium malonate, 100 mM Tris-HCl (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 209648 / Num. obs: 209344 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 46.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.798 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / 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: 15.897 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→20 Å
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Refine LS restraints |
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