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Yorodumi- PDB-1v3h: The roles of Glu186 and Glu380 in the catalytic reaction of soybe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v3h | |||||||||
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Title | The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase | |||||||||
Components | Beta-amylase | |||||||||
Keywords | HYDROLASE / (beta/alpha)8 barrel | |||||||||
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 / SYNCHROTRON / rigid body refinement / Resolution: 1.6 Å | |||||||||
Authors | Kang, Y.N. / Adachi, M. / Utsumi, S. / Mikami, B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The Roles of Glu186 and Glu380 in the Catalytic Reaction of Soybean beta-Amylase. Authors: Kang, Y.N. / Adachi, M. / 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 | 1v3h.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v3h.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v3h_validation.pdf.gz | 759.3 KB | Display | wwPDB validaton report |
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Full document | 1v3h_full_validation.pdf.gz | 767.8 KB | Display | |
Data in XML | 1v3h_validation.xml.gz | 28 KB | Display | |
Data in CIF | 1v3h_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/1v3h ftp://data.pdbj.org/pub/pdb/validation_reports/v3/1v3h | HTTPS FTP |
-Related structure data
Related structure data | 1v3iC 1bybS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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Details | the biological assembly is a monomer |
-Components
#1: Protein | Mass: 55964.188 Da / Num. of mol.: 1 / Mutation: F76L, E186Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: BMY1 / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P10538, beta-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: Chemical | ChemComp-SO4 / #4: 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: 2.25 Å3/Da / Density % sol: 44.91 % |
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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 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.986 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2002 |
Radiation | Monochromator: rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.986 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→99 Å / Num. all: 81131 / Num. obs: 80563 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.043 |
Reflection shell | Resolution: 1.6→1.65 Å / Num. unique all: 7849 / Rsym value: 0.141 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB entry 1BYB Resolution: 1.6→19.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2236708.55 / 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: 59.6967 Å2 / ksol: 0.424446 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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