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Yorodumi- PDB-2e8y: Crystal structure of pullulanase type I from Bacillus subtilis st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8y | ||||||
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Title | Crystal structure of pullulanase type I from Bacillus subtilis str. 168 | ||||||
Components | AmyX protein | ||||||
Keywords | HYDROLASE / multiple domain / beta-alpha-barrel / alpha-amylase-family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Mikami, B. / Malle, D. / Utsumi, S. / Iwamoto, H. / Katsuya, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of pullulanase type I from Bacillus subtilis str. 168 in complex with maltose and alpha-cyclodextrin Authors: Malle, D. / Iwamoto, H. / Katsuya, Y. / Utsumi, S. / Mikami, B. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Overexpression, purification and preliminary X-ray analysis of pullulanase from Bacillus subtilis strain 168 Authors: Malle, D. / Itoh, T. / Hashimoto, W. / Murata, K. / 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 | 2e8y.cif.gz | 303.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8y.ent.gz | 243 KB | Display | PDB format |
PDBx/mmJSON format | 2e8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e8y_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 2e8y_full_validation.pdf.gz | 501.9 KB | Display | |
Data in XML | 2e8y_validation.xml.gz | 59.1 KB | Display | |
Data in CIF | 2e8y_validation.cif.gz | 83.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8y ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8y | HTTPS FTP |
-Related structure data
Related structure data | 2e8zC 2e9bC 2fgzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 81206.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: amyX / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): HMS 174 References: UniProt: O34587, UniProt: C0SPA0*PLUS, pullulanase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 10% PEG 4000, 0.1M sodium acetate buffer, 0.2M magnesium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jan 1, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.3 Å / Num. all: 99401 / Num. obs: 99003 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.314 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FGZ Resolution: 2.11→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3846922.54 / 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: 56.9342 Å2 / ksol: 0.395723 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.11→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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