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Yorodumi- PDB-5wv8: Crystal structure of a mutant insect group III chitinase (CAD1-E2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wv8 | |||||||||||||||
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Title | Crystal structure of a mutant insect group III chitinase (CAD1-E217L) from Ostrinia furnacalis | |||||||||||||||
Components | Chitinase | |||||||||||||||
Keywords | HYDROLASE / Ostrinia furnacalis / chitinase / three-dimensional structure / chitin metabolism | |||||||||||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||||||||
Biological species | Ostrinia furnacalis (Asian corn borer) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.042 Å | |||||||||||||||
Authors | Liu, T. / Zhou, Y. / Yang, Q. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: The deduced role of a chitinase containing two nonsynergistic catalytic domains Authors: Liu, T. / Zhu, W. / Wang, J. / Zhou, Y. / Duan, Y. / Qu, M. / Yang, Q. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wv8.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wv8.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wv8_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 5wv8_full_validation.pdf.gz | 424.9 KB | Display | |
Data in XML | 5wv8_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 5wv8_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wv8 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wv8 | HTTPS FTP |
-Related structure data
Related structure data | 5wupSC 5wusC 5wv9C 5wvbC 5wvfC 5wvgC 5wvhC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54026.371 Da / Num. of mol.: 1 / Fragment: UNP residues 1-482 / Mutation: E217L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: U5LUV7, chitinase |
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#2: 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: 2.32 Å3/Da / Density % sol: 47.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 200mM ammonium sulfate, 100mM Bis-Tris pH 6.6, 21% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 35271 / % possible obs: 94.4 % / Redundancy: 14.1 % / Rsym value: 0.0765 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 12.7 % / Rsym value: 0.371 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5wup Resolution: 2.042→40.099 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.042→40.099 Å
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Refine LS restraints |
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LS refinement shell |
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