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Open data
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Basic information
Entry | Database: PDB / ID: 7ztn | |||||||||
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Title | Crystal structure of fungal CE16 acetyl xylan esterase | |||||||||
![]() | Carbohydrate esterase family 16 protein | |||||||||
![]() | HYDROLASE / acetyl xylan esterase / fungal / hemicellulose | |||||||||
Function / homology | GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / ACETATE ION / : / THIOCYANATE ION / Carbohydrate esterase family 16 protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dimarogona, M. / Kosinas, C. / Pentari, C. / Zerva, A. / Topakas, E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The role of CE16 exo-deacetylases in hemicellulolytic enzyme mixtures revealed by the biochemical and structural study of the novel TtCE16B esterase. Authors: Pentari, C. / Zerva, A. / Kosinas, C. / Karampa, P. / Puchart, V. / Dimarogona, M. / Topakas, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.8 KB | Display | ![]() |
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PDB format | ![]() | 250.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p1gC 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
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 39503.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#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 |
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#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(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 |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 748 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ACT / | ||||||||
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#6: Chemical | #7: Chemical | ChemComp-B3P / | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Potassium thiocyanate, Bis Tris propane, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→162.4 Å / Num. obs: 140699 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 0.99 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Num. unique obs: 6878 / CC1/2: 0.488 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold Resolution: 1.45→79.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.354 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.439 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→79.65 Å
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