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Yorodumi- PDB-5xh8: Aspergillus kawachii beta-fructofuranosidase complexed with glycerol -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xh8 | ||||||
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Title | Aspergillus kawachii beta-fructofuranosidase complexed with glycerol | ||||||
Components | Extracellular invertase | ||||||
Keywords | HYDROLASE / fructooligosaccharides / 1-kestose / GH32 / beta-propeller | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Aspergillus kawachii (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nagaya, M. / Tonozuka, T. | ||||||
Citation | Journal: Biosci. Biotechnol. Biochem. / Year: 2017 Title: Crystal structure of a beta-fructofuranosidase with high transfructosylation activity from Aspergillus kawachii Authors: Nagaya, M. / Kimura, M. / Gozu, Y. / Sato, S. / Hirano, K. / Tochio, T. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xh8.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xh8.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 5xh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xh8_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 5xh8_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 5xh8_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 5xh8_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xh8 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xh8 | HTTPS FTP |
-Related structure data
Related structure data | 5xh9C 5xhaC 3ldkS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 65816.336 Da / Num. of mol.: 1 / Fragment: UNP residues 25-628 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus kawachii (strain NBRC 4308) (mold) Strain: NBRC 4308 / Gene: AKAW_06215 / Production host: Escherichia coli (E. coli) / References: UniProt: G7XM46 | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 3.95 Å3/Da / Density % sol: 68.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium acetate, 2.6 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 13, 2016 |
Radiation | Monochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.11 Å / Num. obs: 61305 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 53.6 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 7.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LDK Resolution: 2.1→47.11 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.127 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.952 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→47.11 Å
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Refine LS restraints |
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