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Yorodumi- PDB-3wf0: Crystal structure of human beta-galactosidase in complex with 6S-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wf0 | ||||||
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Title | Crystal structure of human beta-galactosidase in complex with 6S-NBI-DGJ | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE / TIM-BARREL DOMAIN | ||||||
Function / homology | Function and homology information MPS IV - Morquio syndrome B / response to cortisone / keratan sulfate catabolic process / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / Sialic acid metabolism / heparan sulfate proteoglycan catabolic process / glycosphingolipid catabolic process ...MPS IV - Morquio syndrome B / response to cortisone / keratan sulfate catabolic process / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / Sialic acid metabolism / heparan sulfate proteoglycan catabolic process / glycosphingolipid catabolic process / HS-GAG degradation / galactoside binding / Glycosphingolipid catabolism / beta-galactosidase / vacuole / beta-galactosidase activity / lysosomal lumen / azurophil granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Suzuki, H. / Ohto, U. / Shimizu, T. | ||||||
Citation | Journal: to be published Title: Structural basis of pharmacological chaperoning for human beta-galactosidase Authors: Suzuki, H. / Ohto, U. / Higaki, K. / Mena-Barragan, T. / Aguilar-Moncayo, M. / Ortiz Mellet, C. / Nanba, E. / Garcia Fernandez, J.M. / Suzuki, Y. / Shimizu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wf0.cif.gz | 512.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wf0.ent.gz | 418.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wf0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3wf0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3wf0_validation.xml.gz | 97 KB | Display | |
Data in CIF | 3wf0_validation.cif.gz | 139.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/3wf0 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/3wf0 | HTTPS FTP |
-Related structure data
Related structure data | 3wezC 3wf1C 3wf2C 3wf3C 3wf4C 3thcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 20 molecules ABCD
#1: Protein | Mass: 76618.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELNR1, GLB1 / Production host: Pichia pastoris (fungus) / References: UniProt: P16278, beta-galactosidase #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 1268 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-6DJ / ( #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: 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: 2.64 Å3/Da / Density % sol: 53.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, Ammonium sulfate, HEPES, pH 7.5, vapor diffusion, sittingdrop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 139532 / % possible obs: 90.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3THC Resolution: 2.2→43.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.418 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 109.75 Å2 / Biso mean: 21.643 Å2 / Biso min: 5.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→43.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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