[English] 日本語
Yorodumi- PDB-3wpy: Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wpy | ||||||
---|---|---|---|---|---|---|---|
Title | Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/S200T/F447V/P500S | ||||||
Components | Beta-fructofuranosidaseSucrase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase family 68 / Beta-propeller | ||||||
Function / homology | Function and homology information levansucrase activity / carbohydrate utilization / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Arthrobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yokoi, G. / Mori, M. / Sato, S. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2014 Title: Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 beta-fructofuranosidase Authors: Ohta, Y. / Hatada, Y. / Hidaka, Y. / Shimane, Y. / Usui, K. / Ito, T. / Fujita, K. / Yokoi, G. / Mori, M. / Sato, S. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wpy.cif.gz | 330.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wpy.ent.gz | 266 KB | Display | PDB format |
PDBx/mmJSON format | 3wpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wpy ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wpy | HTTPS FTP |
---|
-Related structure data
Related structure data | 3wpuSC 3wpvC 3wpzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59363.207 Da / Num. of mol.: 3 / Fragment: UNP residues 37-578 / Mutation: T47S/S200T/F447V/P500S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter (bacteria) / Strain: K-1 / Gene: bff / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VW87, beta-fructofuranosidase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM sodium acetate, 22.5% PEG 8000, 300mM Glycine, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2010 |
Radiation | Monochromator: 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→50 Å / Num. obs: 98429 / % possible obs: 97.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.7 / % possible all: 93.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WPU Resolution: 2→36.13 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.965 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 26.291 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|