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Open data
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Basic information
Entry | Database: PDB / ID: 1hvx | ||||||
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Title | BACILLUS STEAROTHERMOPHILUS ALPHA-AMYLASE | ||||||
![]() | ALPHA-AMYLASE | ||||||
![]() | HYDROLASE / GLYCOSYLTRANSFERASE / ALPHA-AMYLASE / STARCH DEGRADATION / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / THERMOSTABILITY | ||||||
Function / homology | ![]() alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suvd, D. / Fujimoto, Z. / Takase, K. / Matsumura, M. / Mizuno, H. | ||||||
![]() | ![]() Title: Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability. Authors: Suvd, D. / Fujimoto, Z. / Takase, K. / Matsumura, M. / Mizuno, H. #1: ![]() Title: Purification, crystallization and preliminary X-ray crystallographic study of alpha-amylase from Bacillus stearothermophilus. Authors: Suvd, D. / Takase, K. / Fujiimoto, Z. / Matsumura, M. / Mizuno, H. #2: ![]() Title: Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution. Authors: Machius, M. / Wiegand, G. / Huber, R. #3: ![]() Title: ACTIVATION OF BACILLUS LICHENIFORMIS ALPHA-AMYLASE THROUGH A DISORDER-->ORDER TRANSITION OF THE SUBSTRATE-BINDING SITE MEDIATED BY A CALCIUM-SODIUM-CALCIUM METAL TRIAD Authors: Machius, M. / Declerck, N. / Huber, R. / Wiegand, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.2 KB | Display | ![]() |
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Full document | ![]() | 411.1 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58890.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: AMYT631 / Plasmid: PTUB617 / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Sequence details | THERE IS A DIFFERENCE BETWEEN THE DEPOSITORS DATA(250Y) AND THE GENETIC SEQUENCE(284D) IN THE ...THERE IS A DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.19 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: SODIUM ACETATE, CALCIUM CLORIDE, 2-PROPANOL, ACARBOSE , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 30530 / Num. obs: 29849 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 2.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.202 / Num. unique all: 3026 / % possible all: 73 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 10.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→8 Å / Rfactor Rfree error: 0.017
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.156 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 10.2 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.185 |