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- PDB-5mgd: STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mgd | |||||||||
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Title | STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH 6-Galactosyl-lactose | |||||||||
![]() | Probable beta-galactosidase A | |||||||||
![]() | HYDROLASE / TIM barrel / GH35 / GLYCOSIDE HYDROLASE / KINETICS / PROTEIN CONFORMATION / carbohydrate metabolism / b-galactosidase / Aspergillus niger / fungal protein / SUBSTRATE SPECIFICITY / prebiotics / galactooligosaccharides / GOS / recombinant / 6-Gal-Lac / 6-Galactosyllactose | |||||||||
Function / homology | ![]() oligosaccharide binding / lactose catabolic process / beta-galactosidase / vacuole / beta-galactosidase activity / polysaccharide catabolic process / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rico-Diaz, A. / Ramirez-Escudero, M. / Vizoso Vazquez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J. | |||||||||
![]() | ![]() Title: Structural features of Aspergillus niger beta-galactosidase define its activity against glycoside linkages. Authors: Rico-Diaz, A. / Ramirez-Escudero, M. / Vizoso-Vazquez, 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 | ![]() | 215.4 KB | Display | ![]() |
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PDB format | ![]() | 168.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 52.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ifpSC ![]() 5iftC ![]() 5ihrC ![]() 5juvC ![]() 5mgcC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 110627.859 Da / Num. of mol.: 1 / Mutation: E298Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 5 types, 10 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | beta-D-galactopyranose-(1-6)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 188 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-DMS / |
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#8: Chemical | ChemComp-CL / |
#9: Chemical | ChemComp-1PE / |
#10: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % / Description: Rod-shaped crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 26% (W/V) PEG 3350, 0.1M BIS-TRIS BUFFER pH 6.5, 0.2M LITHIUM SULPHATE, then soaked in 30mM 6-Galactosyl-lactose, and cryoprotected with 20% (W/V) PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2016 / Details: Kbmirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→82.63 Å / Num. obs: 54536 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 4.2 / CC1/2: 0.936 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IFP Resolution: 2.15→82.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.508 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.197 / 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 mean: 28.762 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→82.63 Å
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Refine LS restraints |
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