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Yorodumi- PDB-3hlk: Crystal structure of human mitochondrial acyl-CoA thioesterase (ACOT2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hlk | ||||||
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Title | Crystal structure of human mitochondrial acyl-CoA thioesterase (ACOT2) | ||||||
Components | Acyl-coenzyme A thioesterase 2, mitochondrial | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / Alternative splicing / Mitochondrion / Polymorphism / Serine esterase / Transit peptide | ||||||
Function / homology | Function and homology information protein targeting to peroxisome / : / palmitoyl-CoA hydrolase / : / very long-chain fatty acid metabolic process / acyl-CoA metabolic process / long-chain fatty acid metabolic process / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / carboxylic ester hydrolase activity ...protein targeting to peroxisome / : / palmitoyl-CoA hydrolase / : / very long-chain fatty acid metabolic process / acyl-CoA metabolic process / long-chain fatty acid metabolic process / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / carboxylic ester hydrolase activity / peroxisomal matrix / fatty acid metabolic process / Peroxisomal protein import / mitochondrial matrix / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Mandel, C.R. / Tweel, B. / Tong, L. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Crystal structure of human mitochondrial acyl-CoA thioesterase (ACOT2) Authors: Mandel, C.R. / Tweel, B. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hlk.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hlk.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hlk ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hlk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49677.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACOT2, PTE2, PTE2A / Production host: Escherichia coli (E. coli) / References: UniProt: P49753, palmitoyl-CoA hydrolase #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: 3 Å3/Da / Density % sol: 58.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 300 mM ammonium citrate, 22% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 67802 / % possible obs: 99.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.0148 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.799 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.697 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.242 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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