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- PDB-5yal: Ferulic acid esterase from Streptomyces cinnamoneus at 1.5 A reso... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yal | ||||||
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Title | Ferulic acid esterase from Streptomyces cinnamoneus at 1.5 A resolution | ||||||
![]() | Esterase | ||||||
![]() | HYDROLASE / Ferulic acid esterase / Catalytic triad / Serine protease | ||||||
Function / homology | Platelet-activating factor acetylhydrolase-like / Platelet-activating factor acetylhydrolase, isoform II / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid catabolic process / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold / ACETATE ION / Esterase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tamura, H. / Uraji, M. / Mizohata, E. / Ogawa, K. / Inoue, T. / Hatanaka, T. | ||||||
![]() | ![]() Title: Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass. Authors: Uraji, M. / Tamura, H. / Mizohata, E. / Arima, J. / Wan, K. / Ogawa, K. / Inoue, T. / Hatanaka, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.5 KB | Display | ![]() |
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PDB format | ![]() | 61.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yaeSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 37065.191 Da / Num. of mol.: 1 / Fragment: UNP residues 42-383 / Mutation: P8A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG 8000, sodium acetate trihydrate, sodium cacodylate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: May 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→42.4 Å / Num. obs: 53162 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YAE Resolution: 1.5→42.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.269 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.749 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→42.39 Å
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Refine LS restraints |
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