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- PDB-8jh9: Structure-based characterization and improvement of an enzymatic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jh9 | |||||||||||||||||||||
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Title | Structure-based characterization and improvement of an enzymatic activity of Acremonium alcalophilum feruloyl esterase | |||||||||||||||||||||
![]() | Feruloyl esterase with ferulic acid | |||||||||||||||||||||
![]() | HYDROLASE / Feruloyl esterase | |||||||||||||||||||||
Function / homology | 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Phienluphon, A. / Kondo, K. / Mikami, B. / Nagata, T. / Katahira, M. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Characterization and Improvement of an Enzymatic Activity of Acremonium alcalophilum Feruloyl Esterase Authors: Phienluphon, A. / Kondo, K. / Mikami, B. / Teo, K.S.K. / Saito, K. / Watanabe, T. / Nagata, T. / Katahira, M. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jh8SC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26974.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#3: Chemical | ChemComp-FER / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M MgCl2, 0.1 M Tris-HCl, and 30% (w/v) PEG4,000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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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: 2→50 Å / Num. obs: 16580 / % possible obs: 97.7 % / Redundancy: 4.21 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.038 / Net I/σ(I): 30.63 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 10.18 / Num. unique obs: 2438 / CC1/2: 0.984 / Rrim(I) all: 0.157 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8JH8 Resolution: 2→41.19 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7087 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: 26.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.19 Å
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Refine LS restraints |
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LS refinement shell |
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