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Yorodumi- PDB-6bjb: Crystal structure of Acat2-C91S thiolase from Ascaris suum in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bjb | ||||||
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Title | Crystal structure of Acat2-C91S thiolase from Ascaris suum in complex with propionyl-CoA and nitrate | ||||||
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: 1.50000626234 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 | 6bjb.cif.gz | 370.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bjb.ent.gz | 245 KB | Display | PDB format |
PDBx/mmJSON format | 6bjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bjb_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6bjb_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6bjb_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 6bjb_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/6bjb ftp://data.pdbj.org/pub/pdb/validation_reports/bj/6bjb | HTTPS FTP |
-Related structure data
Related structure data | 6bj9SC 6bjaC 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
#1: Protein | Mass: 41130.668 Da / Num. of mol.: 2 / Fragment: residues 24-413 / Mutation: C91S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: pET23a-AsAcat2-C91S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: F1KYX0 #2: Chemical | #3: Chemical | ChemComp-NO3 / #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: 2.8 Å3/Da / Density % sol: 56.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium nitrate, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115859 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115859 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→75.11 Å / Num. obs: 144700 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 12.0894204499 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.03 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 14328 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BJ9 Resolution: 1.50000626234→75.1081451893 Å / SU ML: 0.127066613467 / Cross valid method: FREE R-VALUE / σ(F): 1.33444938056 / Phase error: 16.3612163118
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9827862986 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.50000626234→75.1081451893 Å
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Refine LS restraints |
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LS refinement shell |
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