+Open data
-Basic information
Entry | Database: PDB / ID: 1ooy | ||||||
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Title | SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART | ||||||
Components | Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor | ||||||
Keywords | TRANSFERASE / ALPHA/BETA PROTEIN | ||||||
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 body catabolic process / Mitochondrial protein degradation / protein homodimerization activity / mitochondrion Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Coros, A.M. / Swenson, L. / Wolodko, W.T. / Fraser, M.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of the CoA transferase from pig heart to 1.7 A resolution. Authors: Coros, A.M. / Swenson, L. / Wolodko, W.T. / Fraser, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ooy.cif.gz | 214.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ooy.ent.gz | 169.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ooy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/1ooy ftp://data.pdbj.org/pub/pdb/validation_reports/oo/1ooy | HTTPS FTP |
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-Related structure data
Related structure data | 1oozC 1opeC 1m3eS 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 on special symmetry positions |
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Details | The biological assembly is a tetramer, generated by the two-fold axis: -x, -y,z. |
-Components
#1: Protein | Mass: 52293.957 Da / Num. of mol.: 2 / Fragment: succinyl-CoA:3-ketoacid CoA transferase monomer Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: OXCT OR SCOT / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q29551, 3-oxoacid CoA-transferase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-PO4 / | #4: 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: 2.06 Å3/Da / Density % sol: 39.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 2000, sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: BRANDEIS / Detector: CCD / Date: Jul 10, 1998 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 111125 / Num. obs: 100807 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.5 / % possible all: 73.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M3E Resolution: 1.7→19.81 Å / Rfactor Rfree error: 0.002 / 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: 39.4975 Å2 / ksol: 0.359214 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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