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Yorodumi- PDB-1q6d: Crystal structure of Soybean Beta-Amylase Mutant (M51T) with Incr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q6d | |||||||||
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Title | Crystal structure of Soybean Beta-Amylase Mutant (M51T) with Increased pH Optimum | |||||||||
Components | beta-amylase | |||||||||
Keywords | HYDROLASE / BETA-ALPHA-BARRELS / BETA-AMYLASE / MALTOSE COMPLEX / INCREASED pH OPTIMUM | |||||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Glycine max (soybean) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hirata, A. / Adachi, M. / Sekine, A. / Kang, Y.N. / Utsumi, S. / Mikami, B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural and Enzymatic Analysis of Soybean {beta}-Amylase Mutants with Increased pH Optimum Authors: Hirata, A. / Adachi, M. / Sekine, A. / Kang, Y.N. / Utsumi, S. / Mikami, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q6d.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q6d.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 1q6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q6d ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q6d | 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: 55935.078 Da / Num. of mol.: 1 / Mutation: M51T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 References: GenBank: 902938, UniProt: P10538*PLUS, beta-amylase | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose | ||
#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: 2.58 Å3/Da / Density % sol: 51.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 10, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→40.65 Å / Num. all: 52309 / Num. obs: 49751 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 6.9 Å2 / Rsym value: 0.073 |
Reflection shell | Resolution: 1.88→1.94 Å / % possible all: 65.2 |
Reflection | *PLUS Num. measured all: 220571 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 65.2 % / Num. unique obs: 3349 / Num. measured obs: 7247 / Rmerge(I) obs: 0.483 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→14.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 504325.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.1948 Å2 / ksol: 0.342373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.07 Å / Rfactor Rfree: 0.317 / Rfactor Rwork: 0.282 / Num. reflection Rwork: 3176 |