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Yorodumi- PDB-1uh2: Thermoactinomyces vulgaris R-47 alpha-amylase/malto-hexaose complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uh2 | |||||||||
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Title | Thermoactinomyces vulgaris R-47 alpha-amylase/malto-hexaose complex | |||||||||
Components | alpha-amylase I | |||||||||
Keywords | HYDROLASE / starch binding domain | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Abe, A. / Tonozuka, T. / Sakano, Y. / Kamitori, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Complex Structures of Thermoactinomyces vulgaris R-47 alpha-Amylase 1 with Malto-oligosaccharides Demonstrate the Role of Domain N Acting as a Starch-binding Domain Authors: Abe, A. / Tonozuka, T. / Sakano, Y. / Kamitori, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uh2.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uh2.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/1uh2 ftp://data.pdbj.org/pub/pdb/validation_reports/uh/1uh2 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 71108.328 Da / Num. of mol.: 1 / Mutation: D356N, E396Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Strain: R-47 / Plasmid: pUC / Production host: Escherichia coli (E. coli) References: GenBank: 1648826, UniProt: Q60053*PLUS, alpha-amylase | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose | ||||
#3: Polysaccharide | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 20000, MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Method: other / Details: Kondo, S., (2000) Protein Pept.Letters, 7, 197. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→27 Å / Num. all: 43343 / Num. obs: 43343 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 513671 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3506104.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.8466 Å2 / ksol: 0.348938 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 27 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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