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Yorodumi- PDB-2nrb: C28S Mutant of Succinyl-CoA:3-Ketoacid CoA Transferase from Pig Heart -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nrb | ||||||
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Title | C28S Mutant of Succinyl-CoA:3-Ketoacid CoA Transferase from Pig Heart | ||||||
Components | Succinyl-CoA:3-ketoacid-coenzyme A transferase 1 | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Tammam, S.D. / Fraser, M.E. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Identification of the Cysteine Residue Exposed by the Conformational Change in Pig Heart Succinyl-CoA:3-Ketoacid Coenzyme A Transferase on Binding Coenzyme A. Authors: Tammam, S.D. / Rochet, J.C. / 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 | 2nrb.cif.gz | 369.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nrb.ent.gz | 301.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrb ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrb | HTTPS FTP |
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-Related structure data
Related structure data | 2nrcC 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
#1: Protein | Mass: 52277.895 Da / Num. of mol.: 4 / Mutation: C28S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: OXCT1, OXCT, SCOT / Organ: Heart / 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-CL / | #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: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 2000, Tris-HCl, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 29, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 114144 / Num. obs: 114144 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4091 / % possible all: 68.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1M3E Resolution: 2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å
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