[English] 日本語
Yorodumi- PDB-3wf2: Crystal structure of human beta-galactosidase in complex with NBT-DGJ -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wf2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human beta-galactosidase in complex with NBT-DGJ | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE / TIM-BARREL DOMAIN | ||||||
Function / homology | Function and homology information keratan sulfate catabolic process / MPS IV - Morquio syndrome B / response to cortisone / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / Sialic acid metabolism ...keratan sulfate catabolic process / MPS IV - Morquio syndrome B / response to cortisone / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / Sialic acid metabolism / glycosphingolipid catabolic process / 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: 2.3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wf2.cif.gz | 510.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wf2.ent.gz | 416.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wf2_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wf2_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3wf2_validation.xml.gz | 97.9 KB | Display | |
Data in CIF | 3wf2_validation.cif.gz | 137.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/3wf2 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/3wf2 | HTTPS FTP |
-Related structure data
Related structure data | 3wezC 3wf0C 3wf1C 3wf3C 3wf4C 3thcS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 / |
---|
-Non-polymers , 5 types, 1116 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NDJ / ( #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
---|
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
|