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- PDB-3wf3: Crystal structure of human beta-galactosidase mutant I51T in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wf3 | ||||||
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Title | Crystal structure of human beta-galactosidase mutant I51T in complex with Galactose | ||||||
![]() | Beta-galactosidase | ||||||
![]() | HYDROLASE / GLYCOSYL HYDROLASE / TIM-BARREL DOMAIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, H. / Ohto, U. / Shimizu, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 517.4 KB | Display | ![]() |
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PDB format | ![]() | 422.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 538 KB | Display | ![]() |
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Full document | ![]() | 569.6 KB | Display | |
Data in XML | ![]() | 100.8 KB | Display | |
Data in CIF | ![]() | 144.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wezC ![]() 3wf0C ![]() 3wf1C ![]() 3wf2C ![]() 3wf4C ![]() 3thcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 , 1 types, 4 molecules ABCD
#1: Protein | Mass: 76606.297 Da / Num. of mol.: 4 / Mutation: I51T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 20 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#2: Sugar | ChemComp-NAG / #3: Sugar | ChemComp-GAL / |
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-Non-polymers , 4 types, 1448 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.02 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 160267 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.5 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3THC Resolution: 2.15→27.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.538 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 103.95 Å2 / Biso mean: 29.4081 Å2 / Biso min: 13.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→27.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
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