[English] 日本語
Yorodumi- PDB-3pij: beta-fructofuranosidase from Bifidobacterium longum - complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pij | ||||||
---|---|---|---|---|---|---|---|
Title | beta-fructofuranosidase from Bifidobacterium longum - complex with fructose | ||||||
Components | Beta-fructofuranosidase | ||||||
Keywords | HYDROLASE / five-bladed beta-propeller and beta-sandwich domains / glycoside hydrolase family 32 / PROBIOTIC BACTERIA / fructose | ||||||
Function / homology | Function and homology information beta-fructofuranosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Bifidobacterium longum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Bujacz, A. / Bujacz, G. / Redzynia, I. / Krzepkowska-Jedrzejczak, M. / Bielecki, S. | ||||||
Citation | Journal: Febs J. / Year: 2011 Title: Crystal structures of the apo form of beta-fructofuranosidase from Bifidobacterium longum and its complex with fructose Authors: Bujacz, A. / Jedrzejczak-Krzepkowska, M. / Bielecki, S. / Redzynia, I. / Bujacz, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pij.cif.gz | 431.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pij.ent.gz | 355.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pij_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3pij_full_validation.pdf.gz | 469.1 KB | Display | |
Data in XML | 3pij_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 3pij_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3pij ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pij | HTTPS FTP |
-Related structure data
Related structure data | 3pigSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59165.793 Da / Num. of mol.: 2 / Fragment: fructofuranosidase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: KN29.1 / Gene: EF216677 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: A2TLS9, beta-fructofuranosidase #2: Sugar | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.17 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7 Details: 0.4M ammonium chloride, 18% PEG 3350, 0.1M MES pH 7.0, protein concentration 11 mg/ml , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2009 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.4 Å / Num. obs: 84167 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 1.95 / % possible all: 56 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3PIG Resolution: 1.8→28.4 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.013 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.933 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→28.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|