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Yorodumi- PDB-1ua7: Crystal Structure Analysis of Alpha-Amylase from Bacillus Subtili... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ua7 | ||||||||||||
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Title | Crystal Structure Analysis of Alpha-Amylase from Bacillus Subtilis complexed with Acarbose | ||||||||||||
Components | Alpha-amylase | ||||||||||||
Keywords | HYDROLASE / BETA-ALPHA-BARRELS / ACARBOSE / GREEK-KEY MOTIF | ||||||||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Bacillus subtilis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.21 Å | ||||||||||||
Authors | Kagawa, M. / Fujimoto, Z. / Momma, M. / Takase, K. / Mizuno, H. | ||||||||||||
Citation | Journal: J.BACTERIOL. / Year: 2003 Title: Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose Authors: Kagawa, M. / Fujimoto, Z. / Momma, M. / Takase, K. / Mizuno, H. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose Authors: Fujimoto, Z. / Takase, K. / Doui, N. / Momma, M. / Matsumoto, T. / Mizuno, H. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and preliminary X-ray studies of wild type and catalytic-site mutant alpha-amylase from Bacillus subtilis Authors: Mizuno, H. / Morimoto, Y. / Tsukihara, T. / Matsumoto, T. / Takase, K. #3: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1992 Title: Site-directed mutagenesis of active site residues in Bacillus subtilis alpha-amylase Authors: Takase, K. / Matsumoto, T. / Mizuno, H. / Yamane, K. #4: Journal: J.BIOCHEM.(TOKYO) / Year: 1984 Title: Changes in the properties and molecular weights of Bacillus subtilis M-type and N-type alpha-amylases resulting from a spontaneous deletion Authors: Yamane, K. / Hirata, Y. / Furusato, T. / Yamazaki, H. / Nakayama, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ua7.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ua7.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ua7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ua7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1ua7_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1ua7_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 1ua7_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/1ua7 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/1ua7 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46796.984 Da / Num. of mol.: 1 / Fragment: residues 4-425 / Mutation: N356Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pNQ356 / Production host: Bacillus subtilis (bacteria) / Strain (production host): 207-25 / References: UniProt: P00691, alpha-amylase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-quinovopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 442 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.83 Å3/Da / Density % sol: 56.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 3350, calcium chloride, Tris-HCl, acarbose, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.49 Å / Num. all: 31194 / Num. obs: 31194 / % possible obs: 93.7 % / Redundancy: 3.46 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3057 / % possible all: 93.7 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.21→19.97 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.5617 Å2 / ksol: 0.346066 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.21→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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