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Yorodumi- PDB-5hjo: Murine endoplasmic reticulum alpha-glucosidase II with bound subs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hjo | |||||||||
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Title | Murine endoplasmic reticulum alpha-glucosidase II with bound substrate analogue | |||||||||
Components |
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Keywords | HYDROLASE / Enzyme Glycosyl hydrolase / GH31 / Quality control exoglycosidase | |||||||||
Function / homology | Function and homology information mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / carbohydrate metabolic process / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / Golgi apparatus / endoplasmic reticulum / RNA binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.29 Å | |||||||||
Authors | Caputo, A.T. / Roversi, P. / Alonzi, D.S. / Kiappes, J.L. / Zitzmann, N. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structures of mammalian ER alpha-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals. Authors: Caputo, A.T. / Alonzi, D.S. / Marti, L. / Reca, I.B. / Kiappes, J.L. / Struwe, W.B. / Cross, A. / Basu, S. / Lowe, E.D. / Darlot, B. / Santino, A. / Roversi, P. / Zitzmann, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hjo.cif.gz | 725.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hjo.ent.gz | 602.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hjo_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5hjo_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5hjo_validation.xml.gz | 68.9 KB | Display | |
Data in CIF | 5hjo_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/5hjo ftp://data.pdbj.org/pub/pdb/validation_reports/hj/5hjo | HTTPS FTP |
-Related structure data
Related structure data | 5f0eC 5h9oC 5hjrC 5iedC 5ieeC 5iefC 5iegC 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 97894.625 Da / Num. of mol.: 2 / Fragment: UNP Residues 33-944 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q8BHN3, EC: 3.2.1.84 #2: Protein | Mass: 8912.645 Da / Num. of mol.: 2 / Fragment: UNP residues 35-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Plasmid: pHLsec / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: O08795 |
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-Sugars , 3 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | |
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-Non-polymers , 5 types, 676 molecules
#5: Chemical | Mass: 59.044 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C2H3O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: GANAB / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human) #6: Chemical | Mass: 62.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C2H6O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: GANAB / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human) #7: Chemical | ChemComp-FMT / Mass: 46.025 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Formula: CH2O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: GANAB / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human) #9: Chemical | ChemComp-CA / #10: 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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 30 % Morpheus ethylene glycol/PEG 8000 mix, 0.1 M Morpheus carboxylic acids mix, 0.1 M Morpheus buffer system 1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→103.1 Å / Num. obs: 101815 / % possible obs: 96.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.206 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.29→2.297 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.1 / Num. measured obs: 3622 / Num. unique all: 731 / CC1/2: 0.552 / Rsym value: 1.484 / % possible all: 70.6 |
-Processing
Software |
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Refinement | Resolution: 2.29→103.1 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.87 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.214
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Displacement parameters | Biso mean: 46.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→103.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.35 Å / Rfactor Rfree error: 0
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