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Yorodumi- PDB-1v5d: The crystal structure of the active form chitosanase from Bacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v5d | ||||||
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Title | The crystal structure of the active form chitosanase from Bacillus sp. K17 at pH6.4 | ||||||
Components | chitosanase | ||||||
Keywords | HYDROLASE / chitosan degradation / glycosil hydrolase / family 8 | ||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Adachi, W. / Shimizu, S. / Sunami, T. / Fukazawa, T. / Suzuki, M. / Yatsunami, R. / Nakamura, S. / Takenaka, A. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2004 Title: Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17 Authors: Adachi, W. / Sakihama, Y. / Shimizu, S. / Sunami, T. / Fukazawa, T. / Suzuki, M. / Yatsunami, R. / Nakamura, S. / Takenaka, A. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Crystallization and preliminary X-ray analyses of the active and the inactive forms of family GH-8 chitosanase with subclass II specificity from Bacillus sp. strain K17 Authors: Sakihama, Y. / Adachi, W. / Shimizu, S. / Sunami, T. / Fukazawa, T. / Suzuki, M. / Yatsunami, R. / Nakamura, S. / Takenaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v5d.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v5d.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 1v5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/1v5d ftp://data.pdbj.org/pub/pdb/validation_reports/v5/1v5d | 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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 43608.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus sp. (bacteria) / Strain: K17 / References: UniProt: Q9ALZ1*PLUS, chitosanase #2: Chemical | ChemComp-PIN / | #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: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 4000, ammonium sulfate, PIPES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: OXFORD PX210 / Detector: CCD / Date: Mar 4, 2002 |
Radiation | Monochromator: ROTATED-INCLINED SI(111) DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40.33 Å / Num. all: 129478 / Num. obs: 128931 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.53 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.4 / Num. unique all: 12781 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.33 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→40.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.005
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