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Yorodumi- PDB-1ji2: Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ji2 | ||||||
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Title | Improved X-ray Structure of Thermoactinomyces vulgaris R-47 alpha-Amylase 2 | ||||||
Components | ALPHA-AMYLASE II | ||||||
Keywords | HYDROLASE / BETA/ALPHA 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kamitori, S. / Abe, A. / Ohtaki, A. / Kaji, A. / Tonozuka, T. / Sakano, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 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: Journal: J.Mol.Biol. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ji2.cif.gz | 261.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ji2.ent.gz | 209.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ji2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1ji2 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1ji2 | 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: 67554.109 Da / Num. of mol.: 2 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 | #3: Water | ChemComp-HOH / | |
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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: 2.76 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.05 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4403550.32 / 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: 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 |