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Open data
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Basic information
Entry | Database: PDB / ID: 7yc0 | ||||||
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Title | Acetylesterase (LgEstI) W.T. | ||||||
![]() | Alpha/beta hydrolase | ||||||
![]() | HYDROLASE / Esterase / Lipase / pathogen bacteria | ||||||
Function / homology | ACETATE ION / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Do, H. / Lee, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae. Authors: Do, H. / Yoo, W. / Wang, Y. / Nam, Y. / Shin, S.C. / Kim, H.W. / Kim, K.K. / Lee, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.9 KB | Display | ![]() |
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PDB format | ![]() | 164.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 886.4 KB | Display | ![]() |
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Full document | ![]() | 897.4 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 56.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yc4C 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
#1: Protein | Mass: 36348.645 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: F4V47_03290 / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris-HCl, pH 7.0, 0.2M calcium acetate hydrate, 20% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.49 Å / Num. obs: 71847 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2→2.04 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 4652 / CC1/2: 0.961 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: model Resolution: 2→28.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.646 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.165 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.693 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.49 Å
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Refine LS restraints |
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LS refinement shell |
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