+Open data
-Basic information
Entry | Database: PDB / ID: 1ndf | ||||||
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Title | Carnitine Acetyltransferase in Complex with Carnitine | ||||||
Components | Carnitine 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 / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / carnitine metabolic process, CoA-linked / 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 / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / carnitine metabolic process, CoA-linked / 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: 1.9 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 | 1ndf.cif.gz | 269.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndf.ent.gz | 214.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ndf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ndf_validation.pdf.gz | 456.4 KB | Display | wwPDB validaton report |
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Full document | 1ndf_full_validation.pdf.gz | 485.3 KB | Display | |
Data in XML | 1ndf_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 1ndf_validation.cif.gz | 82.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndf ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndf | HTTPS FTP |
-Related structure data
Related structure data | 1ndbSC 1ndiC 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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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: 2.37 Å3/Da / Density % sol: 47.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100mM TRIS, 12%PEG 3350,1mM Carnitine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
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 4, 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: 1.9→20 Å / Num. all: 105409 / Num. obs: 105409 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2 |
Reflection shell | Resolution: 1.9→2.02 Å / % possible all: 92.7 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 347562 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1NDB Resolution: 1.9→19.95 Å / Rfactor Rfree error: 0.003 / 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: 49.4827 Å2 / ksol: 0.35557 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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