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Yorodumi- PDB-1ji1: Crystal Structure Analysis of Thermoactinomyces vulgaris R-47 alp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ji1 | ||||||
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Title | Crystal Structure Analysis of Thermoactinomyces vulgaris R-47 alpha-Amylase 1 | ||||||
Components | ALPHA-AMYLASE I | ||||||
Keywords | HYDROLASE / BETA/ALPHA BARREL | ||||||
Function / homology | Function and homology information neopullulanase / neopullulanase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoactinomyces vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ji1.cif.gz | 289.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ji1.ent.gz | 229.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ji1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ji1_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 1ji1_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 1ji1_validation.xml.gz | 58.8 KB | Display | |
Data in CIF | 1ji1_validation.cif.gz | 91.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1ji1 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1ji1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 71110.297 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: Q60053, alpha-amylase #2: Chemical | ChemComp-CA / #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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG1000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Details: Kondo, S., (2000) Protein Pept. Letters, 7, 197., Kamitori, S., (1995) J. Struct. Biol., 114, 229. |
-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: 1.6→20.46 Å / Num. all: 152851 / Num. obs: 152851 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.061 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 391238 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.69 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→20.46 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2904638.28 / 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: 50.55 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→20.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.182 / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.228 / Rfactor obs: 0.228 |