+Open data
-Basic information
Entry | Database: PDB / ID: 1ndi | ||||||
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Title | Carnitine Acetyltransferase in complex with CoA | ||||||
Components | Carnitine AcetyltransferaseCarnitine O-acetyltransferase | ||||||
Keywords | TRANSFERASE / acetyl transfer / CoA / coenzyme A | ||||||
Function / homology | Function and homology information carnitine O-acetyltransferase / carnitine O-acetyltransferase activity / Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / carnitine metabolic process, CoA-linked / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / fatty acid beta-oxidation using acyl-CoA oxidase / short-chain fatty acid metabolic process / medium-chain fatty acid metabolic process ...carnitine O-acetyltransferase / carnitine O-acetyltransferase activity / Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / carnitine metabolic process, CoA-linked / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / fatty acid beta-oxidation using acyl-CoA oxidase / short-chain fatty acid metabolic process / medium-chain fatty acid metabolic process / Peroxisomal protein import / fatty acid metabolic process / peroxisome / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Jogl, G. / Tong, L. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Crystal Structure of Carnitine Acetyltransferase and Implications for the Catalytic Mechanism and Fatty Acid Transport Authors: Jogl, G. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ndi.cif.gz | 264.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndi.ent.gz | 210.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ndi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndi ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndi | HTTPS FTP |
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-Related structure data
Related structure data | 1ndbSC 1ndfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 67681.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P47934, carnitine O-acetyltransferase #2: Chemical | #3: 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: 2.47 Å3/Da / Density % sol: 49.9 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES, 10%PEG 3350, 1mM AcetylCoA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2002 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 53398 / Num. obs: 53398 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 75 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % possible obs: 85 % / Num. measured all: 135285 / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 75 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1NDB Resolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4726 Å2 / ksol: 0.270785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.6 Å / Luzzati sigma a free: 0.74 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Rfactor obs: 0.27 / Rfactor Rwork: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.42 |