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- PDB-8pc7: STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pc7 | |||||||||
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Title | STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE | |||||||||
![]() | Esterase | |||||||||
![]() | HYDROLASE / Ester Hydrolase / Complex | |||||||||
Function / homology | Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / triglyceride lipase activity / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / Chem-ZK8 / Esterase![]() | |||||||||
Biological species | metagenome (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cea-Rama, I. / Sanz-Aparicio, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Transforming an esterase into an enantioselective catecholase through bioconjugation of a versatile metal-chelating inhibitor. Authors: Fernandez-Lopez, L. / Cea-Rama, I. / Alvarez-Malmagro, J. / Ressmann, A.K. / Gonzalez-Alfonso, J.L. / Coscolin, C. / Shahgaldian, P. / Plou, F.J. / Modregger, J. / Pita, M. / Sanz-Aparicio, J. / Ferrer, 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 | ![]() | 262.4 KB | Display | ![]() |
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PDB format | ![]() | 216 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 50.6 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 40217.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZK8 / #4: Chemical | #5: 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: 2.36 Å3/Da / Density % sol: 47.84 % / Description: Plaque |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 27% PEG3350, 0.1M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2020 / Details: KB focusing mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979181 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.35 Å / Num. obs: 57906 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.057 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4513 / CC1/2: 0.884 / Rpim(I) all: 0.231 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.276 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→47.35 Å
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Refine LS restraints |
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