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Yorodumi- PDB-5xyj: Purification,crystallization and structural analysis of cytoplast... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xyj | ||||||
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Title | Purification,crystallization and structural analysis of cytoplastic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae | ||||||
Components | Acetyl-CoA acetyltransferase | ||||||
Keywords | TRANSFERASE / Acetoacetyl-CoA thiolase / Claisen condension / The mevalonate pathway | ||||||
Function / homology | Function and homology information acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / ergosterol biosynthetic process / fatty acid beta-oxidation / mitochondrion / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Zhou, P.F. | ||||||
Citation | Journal: To Be Published Title: Purification,crystallization and structural analysis of cytoplastic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae Authors: Zhou, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xyj.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyj.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xyj_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 5xyj_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 5xyj_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 5xyj_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyj ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyj | HTTPS FTP |
-Related structure data
Related structure data | 5xz5C 2ib7S 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: 42904.723 Da / Num. of mol.: 2 / Mutation: C91A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ERG10, YPL028W, LPB3 / Plasmid: pET22bN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41338, acetyl-CoA C-acetyltransferase #2: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium citrate (pH 6.5), polyethylene glycol 3350 (19%) PH range: 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 62459 / % possible obs: 98.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Χ2: 1 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3038 / CC1/2: 0.946 / Rpim(I) all: 0.183 / Χ2: 0.987 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IB7 Resolution: 1.93→47.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.607 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.114 / 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: 22.7 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→47.53 Å
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Refine LS restraints |
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