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Yorodumi- PDB-1ven: Crystal Structure Analysis of Y164E/maltose of Bacilus cereus Bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ven | ||||||
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Title | Crystal Structure Analysis of Y164E/maltose of Bacilus cereus Beta-amylase at pH 4.6 | ||||||
Components | Beta-amylase | ||||||
Keywords | HYDROLASE / beta-alpha-barrels / optimum pH / Y164E | ||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / starch binding / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Hirata, A. / Adachi, M. / Utsumi, S. / Mikami, B. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type Authors: Hirata, A. / 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 | 1ven.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ven.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ven.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ven_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 1ven_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 1ven_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 1ven_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1ven ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1ven | HTTPS FTP |
-Related structure data
Related structure data | 1vemC 1veoC 1vepC 1b9zS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 58324.461 Da / Num. of mol.: 1 / Mutation: Y164E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P36924, beta-amylase | ||||
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#2: Sugar | #3: Chemical | ChemComp-CA / | #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: 3 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 6000, ammonium sulfate, potassium phosphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 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 29, 2004 |
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: 1.9→30.5 Å / Num. all: 48233 / Num. obs: 48233 / % possible obs: 87.2 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 7.7 Å2 |
Reflection shell | Resolution: 1.87→1.94 Å / Num. unique all: 2257 / % possible all: 34.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B9Z Resolution: 2.02→14.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 730672.62 / 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: 43.2698 Å2 / ksol: 0.319965 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.02→14.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.15 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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