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- PDB-4iig: Crystal structure of beta-glucosidase 1 from Aspergillus aculeatu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iig | |||||||||
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Title | Crystal structure of beta-glucosidase 1 from Aspergillus aculeatus in complex with D-glucose | |||||||||
![]() | Beta-glucosidase 1 | |||||||||
![]() | HYDROLASE / TIM barrel / High-mannose N-glycosylations / Extracellular | |||||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Suzuki, K. / Sumitani, J. / Kawaguchi, T. / Fushinobu, S. | |||||||||
![]() | ![]() Title: Crystal structures of glycoside hydrolase family 3 beta-glucosidase 1 from Aspergillus aculeatus Authors: Suzuki, K. / Sumitani, J. / Nam, Y.W. / Nishimaki, T. / Tani, S. / Wakagi, T. / Kawaguchi, T. / Fushinobu, S. #1: Journal: Gene / Year: 1996 Title: Cloning and sequencing of the cDNA encoding beta-glucosidase 1 from Aspergillus aculeatus Authors: Kawaguchi, T. / Enoki, T. / Tsurumaki, S. / Sumitani, J. / Ueda, M. / Ooi, T. / Arai, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 381.5 KB | Display | ![]() |
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PDB format | ![]() | 312.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 78.9 KB | Display | |
Data in CIF | ![]() | 116.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4iibC ![]() 4iicC ![]() 4iidC ![]() 4iieC ![]() 4iifC ![]() 4iihC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 91231.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 11 types, 23 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 | 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 | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #8: 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-(1-6)]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 #9: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 #10: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 #11: Sugar | ChemComp-NAG / #13: Sugar | ChemComp-BGC / |
-Non-polymers , 2 types, 1319 molecules ![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#12: Chemical | ChemComp-MRD / ( #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 35% MPD, 0.1M Na-acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / 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. all: 100384 / Num. obs: 99937 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.219 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 4752 / Rsym value: 0.457 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.295→2.355 Å / Total num. of bins used: 20
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