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Yorodumi- PDB-6jaw: Crystal structure of Ostrinia furnacalis Group II chitinase catal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jaw | ||||||
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Title | Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a napthalimide derivative | ||||||
Components | Group II chitinase | ||||||
Keywords | HYDROLASE / inhibitor complex / chitinase | ||||||
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: 1.981 Å | ||||||
Authors | Chen, W. / Zhou, Y. / Yang, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition. Authors: Chen, W. / Zhou, Y. / Yang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jaw.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jaw.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/6jaw ftp://data.pdbj.org/pub/pdb/validation_reports/ja/6jaw | HTTPS FTP |
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-Related structure data
Related structure data | 6javC 6jaxC 6jayC 5y29S 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: 44468.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A0A221ZS22, chitinase |
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#2: Chemical | ChemComp-BBO / |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Sequence details | The residues 1863-1878 (GDKWDSPREQWRKDAN) seriously influenced its expression and crystallization, ...The residues 1863-1878 (GDKWDSPREQ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M sodium chloride, 0.1M Tris (pH 8.5) and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.981→50 Å / Num. obs: 51402 / % possible obs: 100 % / Redundancy: 12.7 % / Rsym value: 0.179 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.981→2.03 Å / Redundancy: 12.6 % / Num. unique obs: 1595 / Rsym value: 1.318 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y29 Resolution: 1.981→43.566 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.981→43.566 Å
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Refine LS restraints |
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LS refinement shell |
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