+Open data
-Basic information
Entry | Database: PDB / ID: 1bfn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX | |||||||||
Components | BETA-AMYLASE | |||||||||
Keywords | HYDROLASE / BETA-AMYLASE / BETA-CYCLODEXTRIN / RECOMBINANT | |||||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Glycine max (soybean) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.07 Å | |||||||||
Authors | Adachi, M. / Mikami, B. / Katsube, T. / Utsumi, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin. Authors: Adachi, M. / Mikami, B. / Katsube, T. / Utsumi, S. #1: Journal: Biochemistry / Year: 1994 Title: Crystal Structures of Soybean Beta-Amylase Reacted with Beta-Maltose and Maltal: Active Site Components and Their Apparent Roles in Catalysis Authors: Mikami, B. / Degano, M. / Hehre, E.J. / Sacchettini, J.C. #2: Journal: Biochemistry / Year: 1993 Title: The 2.0-A Resolution Structure of Soybean Beta-Amylase Complexed with Alpha-Cyclodextrin Authors: Mikami, B. / Hehre, E.J. / Sato, M. / Katsube, Y. / Hirose, M. / Morita, Y. / Sacchettini, J.C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bfn.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bfn.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bfn_validation.pdf.gz | 997.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bfn_full_validation.pdf.gz | 1009.6 KB | Display | |
Data in XML | 1bfn_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 1bfn_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/1bfn ftp://data.pdbj.org/pub/pdb/validation_reports/bf/1bfn | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55965.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P10538, beta-amylase |
---|---|
#2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / pH: 5.4 Details: 49% (NH4)2SO4, 0.1M NAOAC PH 5.4, 18MM 2-MERCAPTOETHANOL, AT 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å |
Reflection | *PLUS Highest resolution: 2.07 Å / Lowest resolution: 10 Å / Num. all: 39214 / Num. obs: 36696 / Observed criterion σ(I): 2 / Num. measured all: 152726 / Rmerge(I) obs: 0.06 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.07→10 Å / Data cutoff low absF: 1 / Cross valid method: POSTERIORI / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.07→2.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|