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- PDB-6frv: Structure of the catalytic domain of Aspergillus niger Glucoamylase -
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Open data
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Basic information
Entry | Database: PDB / ID: 6frv | |||||||||
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Title | Structure of the catalytic domain of Aspergillus niger Glucoamylase | |||||||||
![]() | Glucoamylase | |||||||||
![]() | HYDROLASE / glycosylation / starch degradation / glycoside hydrolase | |||||||||
Function / homology | ![]() glucan 1,4-alpha-glucosidase / polysaccharide metabolic process / glucan 1,4-alpha-glucosidase activity / starch binding / fungal-type vacuole / polysaccharide catabolic process / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Roth, C. / Moroz, O.V. / Ariza, A. / Friis, E.P. / Davies, G.J. / Wilson, K.S. | |||||||||
![]() | ![]() Title: Structural insight into industrially relevant glucoamylases: flexible positions of starch-binding domains. Authors: Roth, C. / Moroz, O.V. / Ariza, A. / Skov, L.K. / Ayabe, K. / Davies, G.J. / Wilson, K.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.3 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.7 KB | Display | ![]() |
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Full document | ![]() | 808.7 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fhvC ![]() 6fhwC ![]() 1agmS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 65823.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: 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 | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60 Å / Num. obs: 19454 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rrim(I) all: 0.19 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 1870 / Rrim(I) all: 1.516 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1agm Resolution: 2.3→59.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.567 / ESU R Free: 0.357 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.17 Å2 / Biso mean: 56.096 Å2 / Biso min: 25.05 Å2
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Refinement step | Cycle: final / Resolution: 2.3→59.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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