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- PDB-8iyb: Structure insight into substrate recognition and catalysis by fer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iyb | |||||||||||||||||||||
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Title | Structure insight into substrate recognition and catalysis by feruloyl esterase from Aspergillus sydowii | |||||||||||||||||||||
![]() | Feruloyl esterase | |||||||||||||||||||||
![]() | HYDROLASE / Feruloyl esterase | |||||||||||||||||||||
Function / homology | ![]() acetylxylan esterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / xylan catabolic process / extracellular region Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Phienluphon, A. / Kondo, K. / Mikami, B. / Nagata, T. / Katahira, M. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii. Authors: Phienluphon, A. / Kondo, K. / Mikami, B. / Nagata, T. / Katahira, M. #1: Journal: Bull Soc Ophtalmol Fr / Year: 1987 Title: [Treatment of vitreous hemorrhages. Rare causes]. Authors: Aracil, P. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.4 KB | Display | ![]() |
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PDB format | ![]() | 202.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
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Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iy8SC ![]() 8iycC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 6 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 30317.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 511 molecules ![](data/chem/img/FER.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% (w/v) PEG 4000, 10mM ferulic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 71862 / % possible obs: 98.2 % / Redundancy: 4.38 % / Biso Wilson estimate: 15.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.033 / Net I/σ(I): 27.35 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 5.89 / Num. unique obs: 33874 / CC1/2: 0.978 / Rrim(I) all: 0.181 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8IY8 Resolution: 1.5→47.32 Å / SU ML: 0.1318 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.8152 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: 21.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.32 Å
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Refine LS restraints |
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LS refinement shell |
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