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Yorodumi- PDB-3iwr: Crystal structure of class I chitinase from Oryza sativa L. japonica -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iwr | ||||||
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Title | Crystal structure of class I chitinase from Oryza sativa L. japonica | ||||||
Components | Chitinase | ||||||
Keywords | HYDROLASE / class I chitinase / Oryza sativa L. japonica / Chitin-binding / Glycosidase | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic process Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Kezuka, Y. / Watanabe, T. / Nonaka, T. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Authors: Kezuka, Y. / Kojima, M. / Mizuno, R. / Suzuki, K. / Watanabe, T. / Nonaka, T. #1: Journal: J.Biochem. / Year: 2008 Title: Role of the loop structure of the catalytic domain in rice class I chitinase Authors: Mizuno, R. / Fukamizo, T. / Sugiyama, S. / Nishizawa, Y. / Kezuka, Y. / Nonaka, T. / Suzuki, K. / Watanabe, T. #2: Journal: Biosci.Biotechnol.Biochem. / Year: 2008 Title: Purification and characterization of a rice class I chitinase, OsChia1b, produced in Escherichia coli Authors: Mizuno, R. / Itoh, Y. / Nishizawa, Y. / Kezuka, Y. / Suzuki, K. / Nonaka, T. / Watanabe, T. #3: Journal: Protein Pept.Lett. / Year: 2004 Title: Crystallization and preliminary X-ray analysis of plant class I chitinase from rice Authors: Kezuka, Y. / Kitazaki, K. / Itoh, Y. / Watanabe, J. / Takaha, O. / Watanabe, T. / Nishizawa, Y. / Nonaka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iwr.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iwr.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/3iwr ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iwr | HTTPS FTP |
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-Related structure data
Related structure data | 2dkvSC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32740.217 Da / Num. of mol.: 2 / Fragment: Chitinase 2, residues 33-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: Cht-2, OsJ_18467 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q7DNA1, chitinase #2: Chemical | #3: Chemical | #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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 11%(w/v) PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→101.53 Å / Num. all: 17963 / Num. obs: 17963 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 39.187 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.57→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1143 / Rsym value: 0.221 / % possible all: 79.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DKV Resolution: 2.57→101.53 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.271 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.615 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.868 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→101.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.57→2.637 Å / Total num. of bins used: 20
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