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- PDB-1ud2: Crystal structure of calcium-free alpha-amylase from Bacillus sp.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ud2 | ||||||
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Title | Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) | ||||||
![]() | amylase | ||||||
![]() | HYDROLASE / calcium-free / alkaline / alpha-amylase | ||||||
Function / homology | ![]() alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nonaka, T. / Fujihashi, M. / Kita, A. / Hagihara, H. / Ozaki, K. / Ito, S. / Miki, K. | ||||||
![]() | ![]() Title: Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites Authors: Nonaka, T. / Fujihashi, M. / Kita, A. / Hagihara, H. / Ozaki, K. / Ito, S. / Miki, K. | ||||||
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 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.7 KB | Display | ![]() |
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Full document | ![]() | 377.1 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ud3C ![]() 1ud4C ![]() 1ud5C ![]() 1ud6C ![]() 1ud8C ![]() 1bliS C: citing same article ( S: Starting model for refinement |
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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: 55145.668 Da / Num. of mol.: 1 / Fragment: residues 1-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.72 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: PEG 8000, sodium acetate, glycerol, sodium cacodylate, Tris-HCl, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE |
Radiation | Monochromator: diamond (4 0 0) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→100 Å / Num. all: 43245 / Num. obs: 43245 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.13→2.17 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2158 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 42444 / % possible obs: 98.1 % / Num. measured all: 783382 |
Reflection shell | *PLUS % possible obs: 95.6 % / Mean I/σ(I) obs: 6.79 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BLI Resolution: 2.13→93.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3167164.03 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2482 Å2 / ksol: 0.395206 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.13→93.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.26 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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