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- PDB-3wpu: Full-length beta-fructofuranosidase from Microbacterium saccharop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wpu | ||||||
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Title | Full-length beta-fructofuranosidase from Microbacterium saccharophilum K-1 | ||||||
![]() | Beta-fructofuranosidase | ||||||
![]() | HYDROLASE / Glycoside hydrolase family 68 / Beta-propeller | ||||||
Function / homology | ![]() levansucrase activity / carbohydrate utilization / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yokoi, G. / Mori, M. / Sato, S. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.3 KB | Display | ![]() |
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PDB format | ![]() | 189.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
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Full document | ![]() | 442.6 KB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 72.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wpvC ![]() 3wpyC ![]() 3wpzC ![]() 3vsrS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59421.285 Da / Num. of mol.: 2 / Fragment: UNP residues 37-578 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 31, 2013 |
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: 1.6→50 Å / Num. all: 135214 / Num. obs: 135214 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.1 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VSR Resolution: 1.6→39.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.562 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.556 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.12 Å
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Refine LS restraints |
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