[English] 日本語
![](img/lk-miru.gif)
- PDB-8iyc: Structure insight into substrate recognition and catalysis by fer... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8iyc | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure insight into substrate recognition and catalysis by feruloyl esterase from Aspergillus sydowii | |||||||||||||||||||||
![]() | Feruloyl esterase | |||||||||||||||||||||
![]() | HYDROLASE / Feruloyl esterase / complex / sinapic acid | |||||||||||||||||||||
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 | ![]()
| |||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 295.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 198.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8iy8SC ![]() 8iybC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 4 types, 401 molecules ![](data/chem/img/SXX.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.41 % |
---|---|
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, 10 mM sinapic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 65419 / % possible obs: 98.2 % / Redundancy: 4.51 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.033 / Net I/σ(I): 26.05 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.61 / Num. unique obs: 10051 / CC1/2: 0.955 / Rrim(I) all: 0.272 / % possible all: 93.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8IY8 Resolution: 1.55→32.63 Å / SU ML: 0.1659 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.2149 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→32.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|