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Yorodumi- PDB-2z8g: Aspergillus niger ATCC9642 isopullulanase complexed with isopanose -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z8g | |||||||||
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Title | Aspergillus niger ATCC9642 isopullulanase complexed with isopanose | |||||||||
Components | Isopullulanase | |||||||||
Keywords | HYDROLASE / isopullulanase / GH49 / dextranase / pullulan / beta-helix / Glycoprotein / Glycosidase / Secreted | |||||||||
Function / homology | Function and homology information isopullulanase / isopullulanase activity / metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Aspergillus niger (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Mizuno, M. / Koide, A. / Yamamura, A. / Akeboshi, H. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49 Authors: Mizuno, M. / Koide, A. / Yamamura, A. / Akeboshi, H. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T. #1: Journal: Eur.J.Biochem. / Year: 2004 Title: Insights into the reaction mechanism of glycosyl hydrolase family 49: Site-directed mutagenesis and substrate preference of isopullulanase Authors: Akeboshi, H. / Tonozuka, T. / Furukawa, T. / Ichikawa, K. / Aoki, H. / Shimonishi, A. / Nishikawa, A. / Sakano, Y. #2: Journal: Biosci.Biotechnol.Biochem. / Year: 2003 Title: Construction of an efficient expression system for Aspergillus isopullulanase in Pichia pastoris, and a simple purification method Authors: Akeboshi, H. / Kashiwagi, Y. / Aoki, H. / Tonozuka, T. / Nishikawa, A. / Sakano, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z8g.cif.gz | 255.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8g.ent.gz | 203.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8g ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8g | HTTPS FTP |
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-Related 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: 60038.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Strain: ATCC9642 / Plasmid: pHIL-S1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: O00105, isopullulanase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: 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: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 8.75% PEG 8000, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 123214 / Num. obs: 123214 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3 / Num. unique all: 11669 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a predicted model generated using the Swiss-model server, Akeboshi et al., Eur. J. Biochem., 271, 4420-4427, 2004 Resolution: 1.7→49.69 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2743571.38 / 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: 45.9137 Å2 / ksol: 0.347184 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→49.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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