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Yorodumi- PDB-5mgd: STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN C... -
+Open data
-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 | |||||||||
Components | Probable beta-galactosidase A | |||||||||
Keywords | 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 | Function and homology information oligosaccharide binding / lactose catabolic process / beta-galactosidase / vacuole / beta-galactosidase activity / polysaccharide catabolic process / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Aspergillus niger CBS 513.88 (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Rico-Diaz, A. / Ramirez-Escudero, M. / Vizoso Vazquez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J. | |||||||||
Citation | Journal: FEBS J. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mgd.cif.gz | 215.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgd.ent.gz | 168.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mgd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5mgd_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5mgd_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 5mgd_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgd ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgd | HTTPS FTP |
-Related structure data
Related structure data | 5ifpSC 5iftC 5ihrC 5juvC 5mgcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 110627.859 Da / Num. of mol.: 1 / Mutation: E298Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger CBS 513.88 (mold) / Gene: lacA, An01g12150 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Variant (production host): BJ3505 / References: UniProt: A2QAN3, beta-galactosidase |
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-Sugars , 5 types, 10 molecules
#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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.12714 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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