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Yorodumi- PDB-3wl0: Crystal structure of Ostrinia furnacalis Group I chitinase cataly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wl0 | |||||||||
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Title | Crystal structure of Ostrinia furnacalis Group I chitinase catalytic domain E148A mutant in complex with a(GlcNAc)2 | |||||||||
Components | Chitinase | |||||||||
Keywords | HYDROLASE / glycosyl hydrolase / insect / Ostrinia furnacalis | |||||||||
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: 2.204 Å | |||||||||
Authors | Chen, L. / Liu, T. / Zhou, Y. / Chen, Q. / Shen, X. / Yang, Q. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting. Authors: Chen, L. / Liu, T. / Zhou, Y. / Chen, Q. / Shen, X. / Yang, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wl0.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wl0.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/3wl0 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/3wl0 | HTTPS FTP |
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-Related structure data
Related structure data | 3w4rSC 3wkzC 3wl1C 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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Unit cell |
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-Components
#1: Protein | Mass: 44937.578 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-407 / Mutation: E148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q2V6H4, chitinase | ||
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#2: Polysaccharide | 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: Sugar | #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: 3.48 Å3/Da / Density % sol: 64.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 100mM HEPES pH 7.9, 23% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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 3, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 31026 / Num. obs: 31013 / % possible obs: 99.89 % / Redundancy: 16.9 % / Biso Wilson estimate: 23.51 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 24.81 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 17 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 12.32 / Rsym value: 0.368 / % possible all: 98.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W4R Resolution: 2.204→38.663 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.06 / 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: 2.204→38.663 Å
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Refine LS restraints |
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LS refinement shell |
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