+Open data
-Basic information
Entry | Database: PDB / ID: 3dlx | ||||||
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Title | Crystal structure of human 3-oxoacid CoA transferase 1 | ||||||
Components | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1 | ||||||
Keywords | TRANSFERASE / OXCT1 / SCOT / Succinyl-CoA:3-ketoacid-coenzyme A transferase 1 / Disease mutation / Mitochondrion / Transit peptide / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Utilization of Ketone Bodies / cellular ketone body metabolic process / 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone catabolic process / CoA-transferase activity / ketone body catabolic process / response to xenobiotic stimulus => GO:0009410 / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus ...Utilization of Ketone Bodies / cellular ketone body metabolic process / 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone catabolic process / CoA-transferase activity / ketone body catabolic process / response to xenobiotic stimulus => GO:0009410 / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / adipose tissue development / response to nutrient / response to activity / response to hormone / brain development / heart development / response to ethanol / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kavanagh, K.L. / Shafqat, N. / Yue, W.W. / Picaud, S. / Murray, J.W. / Maclean, E.M. / von Delft, F. / Roos, A.K. / Arrowsmith, C.H. / Wikstrom, M. ...Kavanagh, K.L. / Shafqat, N. / Yue, W.W. / Picaud, S. / Murray, J.W. / Maclean, E.M. / von Delft, F. / Roos, A.K. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human 3-oxoacid CoA transferase 1. Authors: Kavanagh, K.L. / Shafqat, N. / Yue, W.W. / Picaud, S. / Murray, J.W. / Maclean, E.M. / von Delft, F. / Roos, A.K. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / Bountra, C. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dlx.cif.gz | 350.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dlx.ent.gz | 284 KB | Display | PDB format |
PDBx/mmJSON format | 3dlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/3dlx ftp://data.pdbj.org/pub/pdb/validation_reports/dl/3dlx | HTTPS FTP |
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-Related structure data
Related structure data | 1m3eS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53150.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OXCT1, OXCT, SCOT / Plasmid: pNic-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55809, 3-oxoacid CoA-transferase #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: 2.21 Å3/Da / Density % sol: 44.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2008 |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.11 Å / Num. all: 92253 / Num. obs: 92253 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.9 / Num. unique all: 13203 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M3E Resolution: 2.2→48.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.701 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Extra density in the active site could not be interpreted and was left unmodelled.
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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: 29.557 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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