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- PDB-2f6d: Structure of the complex of a glucoamylase from Saccharomycopsis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f6d | |||||||||
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Title | Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose | |||||||||
![]() | Glucoamylase GLU1 | |||||||||
![]() | HYDROLASE / (alpha-alpha)6 barrel / protein-acarbose complex / sugar tongs | |||||||||
Function / homology | ![]() glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / fungal-type vacuole / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sevcik, J. / Hostinova, E. / Solovicova, A. / Gasperik, J. / Dauter, Z. / Wilson, K.S. | |||||||||
![]() | ![]() Title: Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain. Authors: Sevcik, J. / Hostinova, E. / Solovicova, A. / Gasperik, J. / Dauter, Z. / Wilson, K.S. #1: ![]() Title: Structure of glucoamylase from Saccharomycopsis fibuligera at 1.7 A resolution. Authors: Sevcik, J. / Solovicova, A. / Hostinova, E. / Gasperik, J. / Wilson, K.S. / Dauter, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237 KB | Display | ![]() |
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PDB format | ![]() | 187 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2fbaC ![]() 1ayxS 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
#1: Protein | Mass: 54659.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Polysaccharide | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 50 mM acetate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 9, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9096 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→10 Å / Num. obs: 59266 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.49 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.6→1.62 Å / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 4.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1AYX Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.314 / SU ML: 0.046 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.117 / ESU R Free: 0.077 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.659 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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