[English] 日本語
Yorodumi- PDB-1j10: beta-amylase from Bacillus cereus var. mycoides in complex with GGX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j10 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | beta-amylase from Bacillus cereus var. mycoides in complex with GGX | |||||||||
Components | Beta-amylase | |||||||||
Keywords | HYDROLASE / BETA-AMYLASE / RAW-STARCH BINDING DOMAIN | |||||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / starch binding / polysaccharide catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus cereus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | |||||||||
Authors | Oyama, T. / Miyake, H. / Kusunoki, M. / Nitta, Y. | |||||||||
Citation | Journal: J.BIOCHEM.(TOKYO) / Year: 2003 Title: Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents Authors: Oyama, T. / Miyake, H. / Kusunoki, M. / Nitta, Y. #1: Journal: J.BIOCHEM.(TOKYO) / Year: 1999 Title: Crystal Structure of beta-Amylase from Bacillus cereus var. mycoides at 2.2 A resolution Authors: Oyama, T. / Kusunoki, M. / Kishimoto, Y. / Takasaki, Y. / Nitta, Y. #2: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 1996 Title: Kinetic Study of Active Site Structure of beta-Amylase from Bacillus cereus var. mycoides Authors: Nitta, Y. / Shirakawa, M. / Takasaki, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j10.cif.gz | 421.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j10.ent.gz | 348.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/1j10 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/1j10 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1j0yC 1j0zC 1j11C 1j12C 5bcaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 58358.523 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacillus cereus (bacteria) / Strain: var. mycoides / References: UniProt: P36924, beta-amylase #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-xylopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.5 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 6000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Oyama, T., (1998) Protein Pept.Lett., 5, 349. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 14, 1997 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.6 Å / Num. obs: 154446 / % possible obs: 82.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.217 / % possible all: 60.4 |
Reflection | *PLUS Redundancy: 2.1 % / Num. measured all: 322908 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 60.4 % / Redundancy: 1.6 % / Num. unique obs: 14111 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB ENTRY 5BCA Resolution: 2.1→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|