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- PDB-3wf2: Crystal structure of human beta-galactosidase in complex with NBT-DGJ -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wf2 | ||||||
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Title | Crystal structure of human beta-galactosidase in complex with NBT-DGJ | ||||||
![]() | Beta-galactosidase![]() | ||||||
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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 / heparan sulfate proteoglycan catabolic process / Sialic acid metabolism / HS-GAG degradation ...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 / heparan sulfate proteoglycan catabolic process / Sialic acid metabolism / HS-GAG degradation / glycosphingolipid catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 510 KB | Display | ![]() |
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PDB format | ![]() | 416.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wezC ![]() 3wf0C ![]() 3wf1C ![]() 3wf3C ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 20 molecules ABCD![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | ![]() Mass: 76618.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-NAG / ![]() |
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-Non-polymers , 5 types, 1116 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NDJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NDJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / ![]() #4: Chemical | ChemComp-NDJ / ( #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: 2.66 Å3/Da / Density % sol: 53.72 % |
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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: Feb 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→50 Å / Num. obs: 133461 / % possible obs: 98.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3THC Resolution: 2.3→25.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.849 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.53 Å2 / Biso mean: 31.906 Å2 / Biso min: 12.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
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