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- PDB-3lrk: Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lrk | |||||||||
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Title | Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae | |||||||||
![]() | Alpha-galactosidase 1 | |||||||||
![]() | HYDROLASE / alpha-galactosidase / Tetramer / GH27 / Glycoprotein / Glycosidase | |||||||||
Function / homology | ![]() alpha-galactosidase / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fernandez-Leiro, R. / Pereira-Rodriguez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J. | |||||||||
![]() | ![]() Title: Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases. Authors: Fernandez-Leiro, R. / Pereira-Rodriguez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lrlC ![]() 3lrmC ![]() 1uasS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53127.633 Da / Num. of mol.: 1 / Mutation: I181V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MEL1 / Plasmid: YEpFLAG1 / Production host: ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: 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 |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 439 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-BTB / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Deglycosylated sample. 19% PEG3350, 0.1 M BisTris, 0.2 M SCNK, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→111.521 Å / Num. obs: 42919 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 12 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6150 / Rsym value: 0.457 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UAS Resolution: 1.95→111.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.435 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.147 / 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: 97.61 Å2 / Biso mean: 28.367 Å2 / Biso min: 13.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→111.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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