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- PDB-1j0y: Beta-amylase from Bacillus cereus var. mycoides in complex with g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j0y | ||||||
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Title | Beta-amylase from Bacillus cereus var. mycoides in complex with glucose | ||||||
![]() | Beta-amylase | ||||||
![]() | HYDROLASE / BETA-AMYLASE / RAW-STARCH BINDING DOMAIN | ||||||
Function / homology | ![]() beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / starch binding / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Oyama, T. / Miyake, H. / Kusunoki, M. / Nitta, Y. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 417 KB | Display | ![]() |
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PDB format | ![]() | 342.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1j0zC ![]() 1j10C ![]() 1j11C ![]() 1j12C ![]() 5bcaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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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) ![]() ![]() #2: Sugar | ChemComp-BGC / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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