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Yorodumi- PDB-1jf6: Crystal structure of thermoactinomyces vulgaris r-47 alpha-amylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jf6 | ||||||
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Title | Crystal structure of thermoactinomyces vulgaris r-47 alpha-amylase mutant F286Y | ||||||
Components | ALPHA AMYLASE IIAlpha-amylase | ||||||
Keywords | HYDROLASE / alpha/beta barrel | ||||||
Function / homology | Function and homology information neopullulanase / neopullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoactinomyces vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å | ||||||
Authors | Ohtaki, A. / Kondo, S. / Shimura, Y. / Tonozuka, T. / Sakano, Y. / Kamitori, S. | ||||||
Citation | Journal: CARBOHYDR.RES. / Year: 2001 Title: Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, ...Title: Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs Authors: Ohtaki, A. / Kondo, S. / Shimura, Y. / Tonozuka, T. / Sakano, Y. / Kamitori, S. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Crystal Structure of Thermoactinomyces vulgaris R-47 alpha-Amilase 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jf6.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jf6.ent.gz | 192.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jf6 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jf6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 67570.109 Da / Num. of mol.: 2 / Mutation: F286Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Strain: R-47 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08751, neopullulanase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.66 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG600, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 11 ℃ / Details: Kamitori, S., (1999) J.Mol.Biol., 287, 907. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. all: 131345 / Num. obs: 23309 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 5.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 131344 / Rmerge(I) obs: 0.121 |
-Processing
Software |
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Refinement | Resolution: 3.2→38.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4618975.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.26 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→38.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.204 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.334 / Rfactor Rwork: 0.25 / Rfactor obs: 0.25 |