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Yorodumi- PDB-6bja: Crystal structure of Acat5 thiolase from Ascaris suum in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bja | ||||||
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Title | Crystal structure of Acat5 thiolase from Ascaris suum in complex with coenzyme A | ||||||
Components | Acetyl-CoA acetyltransferase A | ||||||
Keywords | TRANSFERASE / thiolase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Ascaris suum (pig roundworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6000144811 Å | ||||||
Authors | Blaisse, M.R. / Fu, B. / Chang, M.C.Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Structural and Biochemical Studies of Substrate Selectivity in Ascaris suum Thiolases. Authors: Blaisse, M.R. / Fu, B. / Chang, M.C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bja.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bja.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bja_validation.pdf.gz | 751.1 KB | Display | wwPDB validaton report |
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Full document | 6bja_full_validation.pdf.gz | 751.7 KB | Display | |
Data in XML | 6bja_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 6bja_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/6bja ftp://data.pdbj.org/pub/pdb/validation_reports/bj/6bja | HTTPS FTP |
-Related structure data
Related structure data | 6bj9C 6bjbC 2ib8S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41992.234 Da / Num. of mol.: 1 / Fragment: residues 28-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: pET23a-AsAcat5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: F1L3N8 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-COA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2 M sodium malonate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→79.4 Å / Num. obs: 59736 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 17.5342589252 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.67 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 5698 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IB8 Resolution: 1.6000144811→79.3832142521 Å / SU ML: 0.125720945896 / Cross valid method: FREE R-VALUE / σ(F): 1.33499160692 / Phase error: 18.2808442151
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1902809801 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6000144811→79.3832142521 Å
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Refine LS restraints |
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LS refinement shell |
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