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Yorodumi- PDB-1vem: Crystal Structure Analysis of Bacillus Cereus Beta-Amylase at the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vem | |||||||||
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Title | Crystal Structure Analysis of Bacillus Cereus Beta-Amylase at the optimum pH (6.5) | |||||||||
Components | Beta-amylase | |||||||||
Keywords | HYDROLASE / beta-alpha-barrels / optimum pH | |||||||||
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: 1.85 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 | 1vem.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vem.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 1vem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vem_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1vem_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1vem_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 1vem_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1vem ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1vem | HTTPS FTP |
-Related structure data
Related structure data | 1venC 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: 58358.523 Da / Num. of mol.: 1 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: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #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: 6.5 Details: PEG 6000, ammonium sulfate, potassium phosphate, pH 6.5, 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: Sep 2, 2002 |
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: 1.7→27.9 Å / Num. all: 128372 / Num. obs: 63534 / % possible obs: 88.9 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 10.7 Å2 |
Reflection shell | Resolution: 1.72→1.78 Å / Num. unique all: 3193 / % possible all: 44.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B9Z Resolution: 1.85→14.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1652171.59 / 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: 44.2929 Å2 / ksol: 0.311526 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→14.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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