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Yorodumi- PDB-4do4: Pharmacological chaperones for human alpha-N-acetylgalactosaminidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4do4 | |||||||||
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Title | Pharmacological chaperones for human alpha-N-acetylgalactosaminidase | |||||||||
Components | Alpha-N-acetylgalactosaminidase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PHARMACOLOGICAL CHAPERONE / (BETA/ALPHA)8 BARREL / GLYCOSIDASE / CARBOHYDRATE-BINDING PROTEIN / GLYCOPROTEIN / LYSOSOME / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information alpha-N-acetylgalactosaminidase / alpha-N-acetylgalactosaminidase activity / glycolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / carbohydrate catabolic process / lysosome / protein homodimerization activity / extracellular exosome / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | |||||||||
Authors | Clark, N.E. / Garman, S.C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Pharmacological chaperones for human alpha-N-acetylgalactosaminidase Authors: Clark, N.E. / Metcalf, M.C. / Best, D. / Fleet, G.W. / Garman, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4do4.cif.gz | 394 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4do4.ent.gz | 320.3 KB | Display | PDB format |
PDBx/mmJSON format | 4do4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4do4_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4do4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4do4_validation.xml.gz | 42 KB | Display | |
Data in CIF | 4do4_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/4do4 ftp://data.pdbj.org/pub/pdb/validation_reports/do/4do4 | HTTPS FTP |
-Related structure data
Related structure data | 4do5C 4do6C 3h53S S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45582.867 Da / Num. of mol.: 2 / Fragment: UNP residues 18-411 / Mutation: N201Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAGA / Plasmid: pIB/V5-His-TOPO TA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI-FIVE References: UniProt: P17050, alpha-N-acetylgalactosaminidase |
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-Sugars , 4 types, 6 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 #5: Sugar | |
-Non-polymers , 5 types, 1009 molecules
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-ACY / | #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: 3.31 Å3/Da / Density % sol: 62.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: 8-16% PEG3350, 70mM citric acid, 30mM Bis-Tris propane, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2010 / Details: PT COATED MIRROR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→50 Å / Num. obs: 228468 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Χ2: 1.41 / Net I/σ(I): 13.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3H53 Resolution: 1.4→26.63 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.56 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 249.5 Å2 / Biso mean: 31.11 Å2 / Biso min: 11.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→26.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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