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Yorodumi- PDB-6lp1: Crystal structure of acetate:succinate CoA transferase (ASCT) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lp1 | ||||||||||||
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Title | Crystal structure of acetate:succinate CoA transferase (ASCT) from Trypanosoma brucei. | ||||||||||||
Components | Succinyl-CoA:3-ketoacid-coenzyme A transferase | ||||||||||||
Keywords | TRANSFERASE / Trypanosoma brucei / acetate:succinate CoA transferase / mitochondrial enzyme | ||||||||||||
Function / homology | Function and homology information 3-oxoacid CoA-transferase / cellular ketone body metabolic process / succinyl-CoA:3-oxo-acid CoA-transferase activity / CoA-transferase activity / ketone body catabolic process / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||||||||
Authors | Mochizuki, K. / Inaoka, D.K. / Shiba, T. / Fukuda, K. / Kurasawa, H. / Mazet, M. / Millerioux, Y. / Bringaud, F. / Boshart, M. / Balogun, E.O. ...Mochizuki, K. / Inaoka, D.K. / Shiba, T. / Fukuda, K. / Kurasawa, H. / Mazet, M. / Millerioux, Y. / Bringaud, F. / Boshart, M. / Balogun, E.O. / Harada, S. / Hirayama, K. / Kita, K. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2020 Title: The ASCT/SCS cycle fuels mitochondrial ATP and acetate production in Trypanosoma brucei. Authors: Mochizuki, K. / Inaoka, D.K. / Mazet, M. / Shiba, T. / Fukuda, K. / Kurasawa, H. / Millerioux, Y. / Boshart, M. / Balogun, E.O. / Harada, S. / Hirayama, K. / Bringaud, F. / Kita, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lp1.cif.gz | 359.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lp1.ent.gz | 290.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lp1_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6lp1_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6lp1_validation.xml.gz | 66.3 KB | Display | |
Data in CIF | 6lp1_validation.cif.gz | 91.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/6lp1 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/6lp1 | HTTPS FTP |
-Related structure data
Related structure data | 3dlxS 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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Unit cell |
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-Components
#1: Protein | Mass: 51858.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Variant: ILtat 1.4 / Production host: Escherichia coli (E. coli) References: UniProt: D0A680, UniProt: Q386P1*PLUS, 3-oxoacid CoA-transferase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Source details | Protein crystallized and deposited in this structure is derived from Trypanosoma brucei ILtat 1.4 ...Protein crystallized and deposited in this structure is derived from Trypanosoma brucei ILtat 1.4 strain, which is not available at the time of data processing. Database D0A680 is dereived from Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972). | |
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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: 2.22 Å3/Da / Density % sol: 44.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.05M HEPES-NaOH buffer pH 7.4, 18% (w/v) PEG 3350, 0.35M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→50 Å / Num. obs: 123547 / % possible obs: 98.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.01→2.13 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 37706 / CC1/2: 0.698 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DLX Resolution: 2.01→19.97 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.187 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 32.452 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→19.97 Å
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Refine LS restraints |
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