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Yorodumi- PDB-2fba: Glucoamylase from Saccharomycopsis fibuligera at atomic resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fba | ||||||
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Title | Glucoamylase from Saccharomycopsis fibuligera at atomic resolution | ||||||
Components | Glucoamylase GLU1 | ||||||
Keywords | HYDROLASE / (alpha-alpha)6 barrel / TRIS | ||||||
Function / homology | Function and homology information glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Saccharomycopsis fibuligera (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Sevcik, J. / Hostinova, E. / Solovicova, A. / Gasperik, J. / Dauter, Z. / Wilson, K.S. | ||||||
Citation | Journal: Febs J. / Year: 2006 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fba.cif.gz | 235.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fba.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/2fba ftp://data.pdbj.org/pub/pdb/validation_reports/fb/2fba | HTTPS FTP |
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-Related structure data
Related structure data | 2f6dC 1ayxS 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
#1: Protein | Mass: 54659.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomycopsis fibuligera (fungus) / Strain: HUT7212 / Gene: GLU1 / Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08017, glucan 1,4-alpha-glucosidase |
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#2: Chemical | ChemComp-TRS / |
#3: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 50 mM acatate 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.834 Å |
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: 0.834 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→15 Å / Num. all: 184868 / Num. obs: 208793 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.1→1.129 Å / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1AYX Resolution: 1.1→14.8 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.422 / SU ML: 0.021 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.033 / ESU R Free: 0.031 / 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: 12.257 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→14.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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