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- PDB-8he4: The structure of chitin deacetylase Pst_13661 from Puccinia strii... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8he4 | ||||||
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Title | The structure of chitin deacetylase Pst_13661 from Puccinia striiformis f. sp. tritici | ||||||
![]() | Chitin deacetylase | ||||||
![]() | HYDROLASE / Chitin deacetylase / Plant pathogenic fungi / Virulence factor | ||||||
Function / homology | ![]() chitin deacetylase activity / side of membrane / cell wall organization / carbohydrate metabolic process / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, L. / Li, Y.C. / Zhou, Y. / Yang, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of chitin deacetylases to attenuate plant fungal diseases. Authors: Liu, L. / Xia, Y. / Li, Y. / Zhou, Y. / Su, X. / Yan, X. / Wang, Y. / Liu, W. / Cheng, H. / Wang, Y. / Yang, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.6 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8he1C ![]() 8he2C ![]() 8hf9C ![]() 8hfaC ![]() 2iw0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31636.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-8GK / ~{ |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1.1M Sodium malonate, 0.1M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 21798 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 14.24 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 2.9 |
Reflection shell | Resolution: 1.93→1.96 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 1058 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2iw0 Resolution: 1.93→22.17 Å / SU ML: 0.149 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.5355 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→22.17 Å
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Refine LS restraints |
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LS refinement shell |
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