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Yorodumi- PDB-5jyc: Crystal structure of the E153Q mutant of the CFTR inhibitory fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jyc | |||||||||
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Title | Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 14,15-EET hydrolysis intermediate | |||||||||
Components | CFTR inhibitory factor | |||||||||
Keywords | HYDROLASE / epoxide hydrolase / hydroxyalkyl-enzyme intermediate | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hvorecny, K.L. / Madden, D.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Pseudomonas aeruginosa sabotages the generation of host proresolving lipid mediators. Authors: Flitter, B.A. / Hvorecny, K.L. / Ono, E. / Eddens, T. / Yang, J. / Kwak, D.H. / Bahl, C.D. / Hampton, T.H. / Morisseau, C. / Hammock, B.D. / Liu, X. / Lee, J.S. / Kolls, J.K. / Levy, B.D. / ...Authors: Flitter, B.A. / Hvorecny, K.L. / Ono, E. / Eddens, T. / Yang, J. / Kwak, D.H. / Bahl, C.D. / Hampton, T.H. / Morisseau, C. / Hammock, B.D. / Liu, X. / Lee, J.S. / Kolls, J.K. / Levy, B.D. / Madden, D.R. / Bomberger, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jyc.cif.gz | 490.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jyc.ent.gz | 403.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/5jyc ftp://data.pdbj.org/pub/pdb/validation_reports/jy/5jyc | HTTPS FTP |
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-Related structure data
Related structure data | 3kd2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 34163.715 Da / Num. of mol.: 4 / Mutation: E153Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS #2: Chemical | ChemComp-EET / ( #3: Water | ChemComp-HOH / | Nonpolymer details | The ligand EET as a substrate is an epoxide, which is converted into a diol via a two-step reaction ...The ligand EET as a substrate is an epoxide, which is converted into a diol via a two-step reaction which includes a covalent intermediate. The protein plus adduct (C15 atom of EET covalently linked to OD2 atom of ASP 129) is the result of the first step in the reaction. | |
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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: 2.25 Å3/Da / Density % sol: 45.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 8K, calcium chloride, sodium acetate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.41 Å / Num. obs: 82560 / % possible obs: 99.96 % / Redundancy: 6.24 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.27 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.16 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.44 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KD2 Resolution: 2→35.41 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→35.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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