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Yorodumi- PDB-1j0j: Crystal structure of neopullulanase E357Q complex with maltotetraose -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j0j | |||||||||
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Title | Crystal structure of neopullulanase E357Q complex with maltotetraose | |||||||||
Components | neopullulanase | |||||||||
Keywords | HYDROLASE / beta-alpha-barrels | |||||||||
Function / homology | Function and homology information neopullulanase / neopullulanase activity / D-glucose binding / carbohydrate metabolic process / calcium ion binding / protein homodimerization activity / identical protein binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Hondoh, H. / Kuriki, T. / Matsuura, Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase Authors: Hondoh, H. / Kuriki, T. / Matsuura, Y. #1: Journal: J.Biol.Chem. / Year: 1992 Title: Action of neopullulanase. neopullulanase catalyzes both hydrolysis and transglycosylation at alpha-(1,4)- and alpha-(1,6)-glucosidic linkages Authors: Takata, H. / Kuriki, T. / Okada, S. / Takesada, Y. / Iizuka, M. / Minamiura, N. / Imanaka, T. #2: Journal: J.Bacteriol. / Year: 1989 Title: Pattern of action of Bacillus stearothermophilus neopullulanase on pullulan Authors: Imanaka, T. / Kuriki, T. #3: Journal: J.Bacteriol. / Year: 1988 Title: New type of pullulanase from Bacillus stearothermophilus and molecular cloning and expression of the gene in Bacillus subtilis Authors: Kuriki, T. / Okada, S. / Imanaka, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j0j.cif.gz | 255 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j0j.ent.gz | 206.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j0j_validation.pdf.gz | 961.1 KB | Display | wwPDB validaton report |
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Full document | 1j0j_full_validation.pdf.gz | 990.4 KB | Display | |
Data in XML | 1j0j_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 1j0j_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j0j ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j0j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer in the assymetric unit. |
-Components
#1: Protein | Mass: 69141.859 Da / Num. of mol.: 2 / Mutation: E357Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pUC129 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: P38940, neopullulanase #2: Polysaccharide | #3: 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: 2.19 Å3/Da / Density % sol: 43.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, sodium chloride, cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 30357 / % possible obs: 99.7 % / Observed criterion σ(F): 2 |
Reflection shell | Resolution: 2.8→2.97 Å / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 30409 / Num. measured all: 111923 / Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS Lowest resolution: 2.95 Å / % possible obs: 100 % / Rmerge(I) obs: 0.313 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.256 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |