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Yorodumi- PDB-1itc: Beta-Amylase from Bacillus cereus var. mycoides Complexed with Ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1itc | |||||||||
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Title | Beta-Amylase from Bacillus cereus var. mycoides Complexed with Maltopentaose | |||||||||
Components | Beta-Amylase | |||||||||
Keywords | HYDROLASE / BETA-AMYLASE / RAW-STARCH BINDING DOMAIN / MALTOPENTAOSE / CATALYTIC-SITE MUTANT | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Miyake, H. / Kurisu, G. / Kusunoki, M. / Nishimura, S. / Kitamura, S. / Nitta, Y. | |||||||||
Citation | Journal: BIOCHEMISTRY / Year: 2003 Title: Crystal Structure of a Catalytic Site Mutant of beta-Amylase from Bacillus cereus var. mycoides Cocrystallized with Maltopentaose Authors: Miyake, H. / Kurisu, G. / Kusunoki, M. / Nishimura, S. / Kitamura, S. / Nitta, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1itc.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1itc.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 1itc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1itc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1itc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1itc_validation.xml.gz | 25 KB | Display | |
Data in CIF | 1itc_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1itc ftp://data.pdbj.org/pub/pdb/validation_reports/it/1itc | HTTPS FTP |
-Related structure data
Related structure data | 1j18C 1itd 1itj 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 58300.484 Da / Num. of mol.: 1 / Mutation: E172A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: var.mycoides / Plasmid: pET21 / Production host: Escherichia coli (E. coli) References: GenBank: 3925826, UniProt: P36924*PLUS, beta-amylase |
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-Sugars , 4 types, 4 molecules
#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 |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose |
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#5: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
-Non-polymers , 4 types, 418 molecules
#6: Chemical | ChemComp-CA / |
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#7: Chemical | ChemComp-SO4 / |
#8: Chemical | ChemComp-ACY / |
#9: 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: 2.82 Å3/Da / Density % sol: 56.33 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 6000, AMMONIUM SULFATE, ACETATE BUFFER, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 37500 / Num. obs: 37458 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.2 Å2 |
Reflection shell | Resolution: 2.1→2.23 Å / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 2.1 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Lowest resolution: 2.21 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1337989.57 / 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: 59.6531 Å2 / ksol: 0.390611 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 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 Lowest resolution: 30 Å / Num. reflection obs: 37458 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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