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Yorodumi- PDB-5ikx: Crystal structure of the alpha-esterase-7 carboxyl esterase (dime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ikx | |||||||||
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Title | Crystal structure of the alpha-esterase-7 carboxyl esterase (dimer), E3, from Lucilia cuprina | |||||||||
Components | Carboxylic ester hydrolaseCarboxylesterase | |||||||||
Keywords | HYDROLASE / organophosphate / carboxylesterase / oligermerization | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity Similarity search - Function | |||||||||
Biological species | Lucilia cuprina (Australian sheep blowfly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||
Authors | Jackson, C. / Fraser, N. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability. Authors: Fraser, N.J. / Liu, J.W. / Mabbitt, P.D. / Correy, G.J. / Coppin, C.W. / Lethier, M. / Perugini, M.A. / Murphy, J.M. / Oakeshott, J.G. / Weik, M. / Jackson, C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ikx.cif.gz | 453 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ikx.ent.gz | 373.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ikx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ikx ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ikx | HTTPS FTP |
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-Related structure data
Related structure data | 4fngS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66388.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly) Gene: LcaE7 / Production host: Escherichia coli (E. coli) References: UniProt: Q25252, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, 20% PEG 2K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.82655 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82655 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→46.9 Å / Num. obs: 62125 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.19→2.31 Å / Rmerge(I) obs: 0.439 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNG Resolution: 2.19→47.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.304 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 37.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→47.06 Å
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Refine LS restraints |
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