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Yorodumi- PDB-1j0y: Beta-amylase from Bacillus cereus var. mycoides in complex with g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j0y | ||||||
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Title | Beta-amylase from Bacillus cereus var. mycoides in complex with glucose | ||||||
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 / FOURIER SYNTHESIS / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j0y.cif.gz | 417 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j0y.ent.gz | 342.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j0y_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 1j0y_full_validation.pdf.gz | 486.5 KB | Display | |
Data in XML | 1j0y_validation.xml.gz | 74.3 KB | Display | |
Data in CIF | 1j0y_validation.cif.gz | 104.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j0y ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j0y | HTTPS FTP |
-Related structure data
Related structure data | 1j0zC 1j10C 1j11C 1j12C 5bcaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-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: Sugar | ChemComp-BGC / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.83 % | |||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1998 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.5 Å / Num. obs: 135775 / % possible obs: 72.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.214 / % possible all: 53.1 |
Reflection | *PLUS Highest resolution: 2 Å / Redundancy: 1.8 % / Num. measured all: 243229 |
Reflection shell | *PLUS % possible obs: 53.1 % / Redundancy: 1.5 % / Num. unique obs: 12350 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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