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Yorodumi- PDB-1q6f: Crystal Structure of Soybean Beta-Amylase Mutant (E178Y) with Inc... -
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-Basic information
Entry | Database: PDB / ID: 1q6f | |||||||||
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Title | Crystal Structure of Soybean Beta-Amylase Mutant (E178Y) with Increased pH Optimum at pH 7.1 | |||||||||
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: 2.1 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 | 1q6f.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q6f.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q6f ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q6f | 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: 55999.230 Da / Num. of mol.: 1 / Mutation: E178Y 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 | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose | ||||||
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | GLC 496 AND ALTERNATE POSITION A OF BGC 497 ARE BOUND EACH OTHER. ALSO, GLC 496 AND ALTERNATE ...GLC 496 AND ALTERNATE POSITION A OF BGC 497 ARE BOUND EACH OTHER. ALSO, GLC 496 AND ALTERNATE POSITION B OF GLC 1497, GLC 498 AND 499 WHICH PLACE ALTERNATE POSITION A, GLC 498 AND 499 WHICH PLACE ALTERNATE POSITION B ARE BOUND EACH OTHER. | Sequence details | THIS CONFLICT BASED ON A REASONABLE SPECIFIC ACTIVITY OF CRUDE EXTRACT. THE REFFERENCE IS JOURNAL ...THIS CONFLICT BASED ON A REASONABLE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / 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: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 31, 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: 1.99→40.65 Å / Num. all: 44346 / Num. obs: 39656 / % possible obs: 89.4 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 8.2 Å2 / Rsym value: 0.084 |
Reflection shell | Resolution: 1.99→2.06 Å / % possible all: 55.9 |
Reflection | *PLUS Num. measured all: 203117 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 55.9 % / Num. unique obs: 2499 / Num. measured obs: 4842 / Rmerge(I) obs: 0.593 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 498594.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.5048 Å2 / ksol: 0.327574 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.17 Å / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.243 / Num. reflection Rwork: 2290 |