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Open data
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Basic information
| Entry | Database: PDB / ID: 7qqg | ||||||
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| Title | Crystal structure of MYORG bound to 1-deoxygalactonojirimycin | ||||||
Components | Myogenesis-regulating glycosidase | ||||||
Keywords | HYDROLASE / GH31 / Glycoside hydrolase / MYORG / NET37 / galactosidase | ||||||
| Function / homology | Function and homology informationHydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / positive regulation of insulin-like growth factor receptor signaling pathway / hydrolase activity, hydrolyzing O-glycosyl compounds / skeletal muscle fiber development / nuclear membrane / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum membrane Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Meek, R.W. / Davies, G.J. | ||||||
| Funding support | United Kingdom, 1items
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Citation | Journal: Plos Biol. / Year: 2022Title: The primary familial brain calcification-associated protein MYORG is an alpha-galactosidase with restricted substrate specificity. Authors: Meek, R.W. / Brockerman, J. / Fordwour, O.B. / Zandberg, W.F. / Davies, G.J. / Vocadlo, D.J. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7qqg.cif.gz | 895.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7qqg.ent.gz | 724.8 KB | Display | PDB format |
| PDBx/mmJSON format | 7qqg.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7qqg_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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| Full document | 7qqg_full_validation.pdf.gz | 3.8 MB | Display | |
| Data in XML | 7qqg_validation.xml.gz | 95.1 KB | Display | |
| Data in CIF | 7qqg_validation.cif.gz | 123.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqg ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqg | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7qqfC ![]() 7qqhC ![]() 2f2hS C: citing same article ( S: Starting model for refinement |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
| #1: Protein | Mass: 72463.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYORG, KIAA1161 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi FiveReferences: UniProt: Q6NSJ0, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Sugars , 3 types, 17 molecules 
| #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 239 molecules 




| #5: Chemical | ChemComp-DGJ / ( #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.74 % |
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| Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES pH 7.0, 10% PEG MME5000, 5% tasimate pH 7.0 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
| Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020 | ||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
| Reflection | Resolution: 2.43→69.75 Å / Num. obs: 127078 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.073 / Rrim(I) all: 0.103 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 2F2H Resolution: 2.43→69.75 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.247 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.249 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 56.614 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.43→69.75 Å
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| Refine LS restraints |
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Movie
Controller
About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
United Kingdom, 1items
Citation


PDBj


Trichoplusia ni (cabbage looper)