+Open data
-Basic information
Entry | Database: PDB / ID: 7y0b | ||||||
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Title | Crystal structure of human short-chain acyl-CoA dehydrogenase | ||||||
Components | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Apo | ||||||
Function / homology | Function and homology information butyrate catabolic process / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty acid beta-oxidation / flavin adenine dinucleotide binding / mitochondrial matrix ...butyrate catabolic process / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty acid beta-oxidation / flavin adenine dinucleotide binding / mitochondrial matrix / centrosome / mitochondrion / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.076 Å | ||||||
Authors | Huang, Y. / Xu, Y. / Li, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human short-chain acyl-coA dehydrogenase Authors: Xu, Y. / Huang, Y. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y0b.cif.gz | 308.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y0b.ent.gz | 247.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/7y0b ftp://data.pdbj.org/pub/pdb/validation_reports/y0/7y0b | HTTPS FTP |
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-Related structure data
Related structure data | 2vigS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43024.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACADS / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P16219, short-chain acyl-CoA dehydrogenase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-7R3 / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 4% Tacsimate, 12% PEG3350, pH 5.0, 2 mM EMPA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.076→39.17 Å / Num. obs: 104537 / % possible obs: 96.75 % / Redundancy: 12.8 % / CC1/2: 0.993 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 2.076→2.15 Å / Num. unique obs: 8418 / CC1/2: 0.799 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VIG Resolution: 2.076→39.17 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.58 / Stereochemistry target values: ML
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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 max: 65.94 Å2 / Biso mean: 20.9175 Å2 / Biso min: 7.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.076→39.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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