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Yorodumi- PDB-7kyd: Drosophila melanogaster long-chain fatty-acyl-CoA synthetase CG6178 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kyd | |||||||||
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Title | Drosophila melanogaster long-chain fatty-acyl-CoA synthetase CG6178 | |||||||||
Components | Long-chain fatty-acyl-CoA synthetase CG6178 | |||||||||
Keywords | LIGASE / luciferase / HYDROLASE | |||||||||
Function / homology | Function and homology information fatty acid ligase activity / long-chain fatty acid-CoA ligase activity / fatty-acyl-CoA biosynthetic process / CoA-ligase activity / acyl-CoA metabolic process / long-chain fatty acid metabolic process / acyltransferase activity / peroxisome / fatty acid biosynthetic process Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Adams, S.T. / Zephyr, J. / Bohn, M.F. / Schiffer, C.A. / Miller, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biorxiv / Year: 2023 Title: FruitFire: a luciferase based on a fruit fly metabolic enzyme. Authors: Adams, S.T. / Zephyr, J. / Bohn, M.F. / Schiffer, C.A. / Miller, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kyd.cif.gz | 144 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kyd.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/7kyd ftp://data.pdbj.org/pub/pdb/validation_reports/ky/7kyd | HTTPS FTP |
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-Related structure data
Related structure data | 4g36S 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: 60421.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG6178, FACL, CG6178, Dmel_CG6178 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9VCC6, long-chain-fatty-acid-CoA ligase |
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#2: Chemical | ChemComp-C5Y / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 28% (w/v) PEG 3350, 0.1M Tris Buffer pH 7.5, 0.2M Ammonium Sulfate, 10mM ATP disodium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.498→30.72 Å / Num. obs: 17684 / % possible obs: 99.72 % / Redundancy: 5.6 % / Biso Wilson estimate: 36.33 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.46 |
Reflection shell | Resolution: 2.498→2.54 Å / Mean I/σ(I) obs: 2.95 / Num. unique obs: 2851 / Rrim(I) all: 0.671 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G36 Resolution: 2.5→30.72 Å / SU ML: 0.3358 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4059 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30.72 Å
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Refine LS restraints |
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LS refinement shell |
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