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Yorodumi- PDB-3igu: Crystal structure of human alpha-N-acetylgalactosaminidase, coval... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3igu | |||||||||
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Title | Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate | |||||||||
Components | Alpha-N-acetylgalactosaminidase | |||||||||
Keywords | HYDROLASE / GLYCOPROTEIN / CARBOHYDRATE-BINDING PROTEIN / GLYCOSIDASE / LYSOSOMAL ENZYME / (BETA/ALPHA)8 BARREL / Schindler disease / Kanzaki disease / Disease mutation / Disulfide bond / Epilepsy / Lysosome / Phosphoprotein | |||||||||
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: 2.15 Å | |||||||||
Authors | Clark, N.E. / Garman, S.C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases Authors: Clark, N.E. / 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 | 3igu.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3igu.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 3igu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3igu_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3igu_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3igu_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 3igu_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/3igu ftp://data.pdbj.org/pub/pdb/validation_reports/ig/3igu | HTTPS FTP |
-Related structure data
Related structure data | 3h53SC 3h54C 3h55C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45582.867 Da / Num. of mol.: 2 / Mutation: N201Q Source method: isolated from a genetically manipulated source Details: Selected with blastocidin / 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 , 5 types, 8 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 | ||||||
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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 #6: Sugar | #7: Sugar | |
-Non-polymers , 2 types, 690 molecules
#5: Chemical | ChemComp-GOL / #8: 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: 3.21 Å3/Da / Density % sol: 61.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 9, 2009 |
Radiation | Monochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 62455 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Χ2: 1.014 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6056 / Rsym value: 0.634 / Χ2: 1.025 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3H53 Resolution: 2.15→45.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.717 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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 max: 114.5 Å2 / Biso mean: 28.732 Å2 / Biso min: 8.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→45.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.149→2.205 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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