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Yorodumi- PDB-2dkv: Crystal structure of class I chitinase from Oryza sativa L. japonica -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dkv | ||||||
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Title | Crystal structure of class I chitinase from Oryza sativa L. japonica | ||||||
Components | chitinase | ||||||
Keywords | HYDROLASE / class I chitinase / whole structure / Oryza sativa L. japonica | ||||||
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 / SAD / Resolution: 2 Å | ||||||
Authors | Kezuka, Y. / Nishizawa, 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: Mol.Gen.Genet. / Year: 1993 Title: Sequence variation, differential expression and chromosomal location of rice chitinase genes Authors: Nishizawa, Y. / Kishimoto, N. / Saito, A. / Hibi, T. #2: 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 | 2dkv.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dkv.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 2dkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dkv_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 2dkv_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 2dkv_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2dkv_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/2dkv ftp://data.pdbj.org/pub/pdb/validation_reports/dk/2dkv | 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 linker peptide is missing due to poor electron density in the unit cell; there are two possible different ways of connecting the catalytic and chitin-binding domains to complete the full-length structure as a biological unit. The deposited coordinates in the asymmetric unit stand for one candidate set of the two possible combinations. The other combination can be generated by moving the chitin-binding domain by the operation: y+1/2, -x+1/2, z+1/4. |
-Components
#1: Protein | Mass: 32740.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Species: Oryza sativa / Strain: Japonica / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) References: GenBank: 407472, UniProt: Q7DNA1*PLUS, chitinase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8%(w/v) PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2004 |
Radiation | Monochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.22 Å / Num. all: 19363 / Num. obs: 19363 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 25.237 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1381 / Rsym value: 0.238 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→33.22 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.606 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.184 / ESU R Free: 0.163 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.254 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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