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- PDB-1ukp: Crystal structure of soybean beta-amylase mutant substituted at s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ukp | ||||||
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Title | Crystal structure of soybean beta-amylase mutant substituted at surface region | ||||||
![]() | Beta-amylase | ||||||
![]() | HYDROLASE / (alpha/beta)8 barrel | ||||||
Function / homology | ![]() beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, Y.N. / Adachi, M. / Mikami, B. / Utsumi, S. | ||||||
![]() | ![]() Title: Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues Authors: Kang, Y.N. / Adachi, M. / Mikami, B. / Utsumi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 407.6 KB | Display | ![]() |
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PDB format | ![]() | 332.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ukoC ![]() 1bybS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | the biological assembly is a monomer |
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Components
#1: Protein | Mass: 56033.168 Da / Num. of mol.: 4 / Mutation: D374Y / L481R / P487D / K462S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.68 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD PX210 / Detector: CCD / Date: Apr 17, 2002 |
Radiation | Monochromator: rotating-inclining double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.98 Å / Num. all: 335804 / Num. obs: 137751 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 2.44 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.121 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.383 / Num. unique all: 13776 / % possible all: 95.3 |
Reflection | *PLUS Num. measured all: 335804 |
Reflection shell | *PLUS % possible obs: 95.3 % / Num. unique obs: 13776 / Num. measured obs: 33459 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BYB Resolution: 2.1→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1432544.57 / 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: 71.9499 Å2 / ksol: 0.455532 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 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: 2.1 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.2345 / Rfactor Rwork: 0.2001 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.17 Å / Num. reflection Rwork: 11208 |