[English] 日本語
Yorodumi- PDB-3vss: Microbacterium saccharophilum K-1 beta-fructofuranosidase catalyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vss | ||||||
---|---|---|---|---|---|---|---|
Title | Microbacterium saccharophilum K-1 beta-fructofuranosidase catalytic domain complexed with fructose | ||||||
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: 1.97 Å | ||||||
Authors | Tonozuka, T. / Tamaki, A. / Yokoi, G. / Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Ohta, Y. / Hidaka, Y. / Katayama, K. / Hatada, Y. ...Tonozuka, T. / Tamaki, A. / Yokoi, G. / Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Ohta, Y. / Hidaka, Y. / Katayama, K. / Hatada, Y. / Ito, T. / Fujita, K. | ||||||
Citation | Journal: Enzyme.Microb.Technol. / Year: 2012 Title: Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 beta-fructofuranosidase Authors: Tonozuka, T. / Tamaki, A. / Yokoi, G. / Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Ohta, Y. / Hidaka, Y. / Katayama, K. / Hatada, Y. / Ito, T. / Fujita, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vss.cif.gz | 118 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vss.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/3vss ftp://data.pdbj.org/pub/pdb/validation_reports/vs/3vss | HTTPS FTP |
---|
-Related structure data
Related structure data | 3vsrSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54539.672 Da / Num. of mol.: 1 / Fragment: UNP residues 37-532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter (bacteria) / Strain: K-1 / Gene: bff / Production host: Bacillus subtilis (bacteria) / Strain (production host): ISW1214 / References: UniProt: Q8VW87, beta-fructofuranosidase | ||
---|---|---|---|
#2: Sugar | ChemComp-FRU / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM sodium acetate pH 5.5, 22.5% polyethylene glycol 8000, 300mM glycine, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 33971 / % possible obs: 98.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.97→2.04 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.6 / % possible all: 96.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VSR Resolution: 1.97→39.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.97 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.167 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.485 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→39.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
|