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Yorodumi- PDB-5wvf: Crystal structure of a mutant insect group III chitinase (CAD2-E6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wvf | |||||||||||||||
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Title | Crystal structure of a mutant insect group III chitinase (CAD2-E647L) 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: 2.399 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 | 5wvf.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wvf.ent.gz | 134 KB | Display | PDB format |
PDBx/mmJSON format | 5wvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wvf ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wvf | HTTPS FTP |
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-Related structure data
Related structure data | 5wupC 5wusSC 5wv8C 5wv9C 5wvbC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 52409.617 Da / Num. of mol.: 1 / Fragment: UNP residues 528-987 / Mutation: E647L 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: Sugar | ChemComp-NAG / |
#3: 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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 200mM tri-sodium citrate dihydrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.399→30 Å / Num. obs: 18731 / % possible obs: 99.6 % / Redundancy: 13.5 % / Rsym value: 0.067 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.399→2.44 Å / Redundancy: 13.9 % / Rsym value: 0.381 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5wus Resolution: 2.399→28.883 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.399→28.883 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.2492 Å / Origin y: 17.2832 Å / Origin z: 18.2217 Å
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Refinement TLS group | Selection details: all |