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- PDB-5xz5: Purification,crystallization and structural analysis of cytoplast... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xz5 | ||||||
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Title | Purification,crystallization and structural analysis of cytoplastic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae | ||||||
![]() | Acetyl-CoA acetyltransferase | ||||||
![]() | TRANSFERASE / Acetoacetyl-CoA thiolase / Claisen condension / The mevalonate pathway | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, P.F. / Zhu, Z.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 127 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.5 KB | Display | ![]() |
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Full document | ![]() | 446.9 KB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xyjC ![]() 2ib7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43074.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: ERG10, YPL028W, LPB3 / Plasmid: pET22bN / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium citrate (pH 7.0), 17% polyethylene glycol 3350 PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 43320 / % possible obs: 99.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Χ2: 0.99 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2111 / CC1/2: 0.911 / Rpim(I) all: 0.192 / Χ2: 1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IB7 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.583 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.194 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.736 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→50 Å
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Refine LS restraints |
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