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- PDB-1ji2: Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ji2 | ||||||
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Title | Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha-Amylase 2 | ||||||
![]() | ALPHA-AMYLASE II | ||||||
![]() | HYDROLASE / BETA/ALPHA BARREL | ||||||
Function / homology | ![]() neopullulanase / neopullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamitori, S. / Abe, A. / Ohtaki, A. / Kaji, A. / Tonozuka, T. / Sakano, Y. | ||||||
![]() | ![]() Title: Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution. Authors: Kamitori, S. / Abe, A. / Ohtaki, A. / Kaji, A. / Tonozuka, T. / Sakano, Y. #1: ![]() Title: Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution Authors: Kamitori, S. / Kondo, S. / Okuyama, K. / Yokota, T. / Shimura, Y. / Tonozuka, T. / Sakano, 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 | ![]() | 261.8 KB | Display | ![]() |
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PDB format | ![]() | 209.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 464.8 KB | Display | |
Data in XML | ![]() | 52.3 KB | Display | |
Data in CIF | ![]() | 76.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 67554.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 6 / Method: vapor diffusion, sitting drop / Details: Kamitori, S., (1995) J.Struct.Biol., 114, 229. | ||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37.05 Å / Num. all: 66868 / Num. obs: 66868 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.062 |
Reflection | *PLUS Lowest resolution: 37 Å / Num. measured all: 362110 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.42 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.42 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→37.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 37 Å / Rfactor obs: 0.179 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.199 / Rfactor obs: 0.199 |