+Open data
-Basic information
Entry | Database: PDB / ID: 5bca | ||||||
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Title | BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES | ||||||
Components | PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.) | ||||||
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 / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Oyama, T. / Kusunoki, M. / Kishimoto, Y. / Takasaki, Y. / Nitta, Y. | ||||||
Citation | 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. #1: Journal: Protein Pept.Lett. / Year: 1998 Title: Crystallization and Preliminary X-Ray Analysis of Beta-Amylase from Bacillus Cereus Var. Mycoides 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. #3: Journal: Biosci.Biotechnol.Biochem. / Year: 1996 Title: Cloning, Sequencing, and Expression of a Beta-Amylase Gene from Bacillus Cereus Var. Mycoides and Characterization of its Products Authors: Yamaguchi, T. / Matsumoto, Y. / Shirakawa, M. / Kibe, M. / Hibino, T. / Kozaki, S. / Takasaki, Y. / Nitta, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bca.cif.gz | 419.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bca.ent.gz | 344.2 KB | Display | PDB format |
PDBx/mmJSON format | 5bca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bca_validation.pdf.gz | 399.1 KB | Display | wwPDB validaton report |
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Full document | 5bca_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 5bca_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 5bca_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/5bca ftp://data.pdbj.org/pub/pdb/validation_reports/bc/5bca | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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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) / Cellular location: EXTRACELLULAR / Variant: MYCOIDES / Strain: BACILLUS CEREUS References: UniProt: Q9Z4N9, UniProt: P36924*PLUS, beta-amylase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % | |||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | |||||||||||||||||||||||||
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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: PHOTON FACTORY / Detector: WEISSENBERG IMAGE PLATE / Details: BENT QUARTZ CRYSTAL |
Radiation | Monochromator: PHOTON FACTORY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→95.3 Å / Num. obs: 113923 / % possible obs: 81.5 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.1 / % possible all: 71.9 |
Reflection | *PLUS Num. measured all: 649891 |
Reflection shell | *PLUS % possible obs: 71.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.25
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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