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Yorodumi- PDB-5wvb: Crystal structure of a mutant insect group III chitinase complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wvb | |||||||||||||||
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Title | Crystal structure of a mutant insect group III chitinase complex with (GlcNAc)6 (CAD1-E217L-(GlcNAc)6 ) from Ostrinia furnacalis | |||||||||||||||
Components | Chitinase | |||||||||||||||
Keywords | HYDROLASE / Ostrinia furnacalis / chitinase / three-dimensional structure / chitin metabolism / (GlcNAc)6 | |||||||||||||||
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: 3.099 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 | 5wvb.cif.gz | 172.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wvb.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wvb ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wvb | HTTPS FTP |
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-Related structure data
Related structure data | 5wupSC 5wusC 5wv8C 5wv9C 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: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 200 mM ammonium sulfate, 100 mM 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: 0.97911 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: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 3.099→50 Å / Num. obs: 9906 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rsym value: 0.115 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.099→3.15 Å / Redundancy: 9.3 % / Rsym value: 0.444 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5wup Resolution: 3.099→49.334 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.099→49.334 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: -22.1024 Å / Origin y: 17.0503 Å / Origin z: 18.8177 Å
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Refinement TLS group | Selection details: all |