[English] 日本語
Yorodumi- PDB-5y2a: Crystal structure of Ostrinia furnacalis Group II chitinase catal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y2a | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 2 | |||||||||
Components | insect group II chitinase | |||||||||
Keywords | HYDROLASE / GH18 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: 1.9 Å | |||||||||
Authors | Chen, W. / Qu, M.B. / Zhou, Y. / Yang, Q. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural analysis of group II chitinase (ChtII) catalysis completes the puzzle of chitin hydrolysis in insects Authors: Chen, W. / Qu, M. / Zhou, Y. / Yang, Q. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5y2a.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5y2a.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 5y2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y2a ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y2a | HTTPS FTP |
---|
-Related structure data
Related structure data | 5y29C 5y2bC 5y2cC 1guvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43471.051 Da / Num. of mol.: 2 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*PLUS, chitinase #2: Polysaccharide | 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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium acetate, 0.1M Bis-Tris, 45% 2-methyl-2,4-pentadiol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 68407 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Χ2: 1.004 / Net I/σ(I): 4.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GUV Resolution: 1.9→50 Å / Cross valid method: NONE
| |||||||||||||||||||||
Displacement parameters | Biso max: 83.23 Å2 / Biso mean: 22.2633 Å2 / Biso min: 9.09 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| |||||||||||||||||||||
LS refinement shell | Resolution: 1.8994→1.9469 Å
|