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- PDB-4wyr: Crystal structure of thiolase mutation (V77Q,N153Y,A286K) from Cl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wyr | ||||||
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Title | Crystal structure of thiolase mutation (V77Q,N153Y,A286K) from Clostridium acetobutylicum | ||||||
![]() | Acetyl-CoA acetyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Kim, K.J. | ||||||
![]() | ![]() Title: Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum Authors: Kim, S. / Jang, Y.S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Hong Lim, J. / Cho, C. / Shin Ryu, Y. / Kuk Lee, S. / Lee, S.Y. / Kim, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.7 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.7 KB | Display | ![]() |
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Full document | ![]() | 470.3 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wysC ![]() 4xl2C ![]() 4xl3C ![]() 4xl4C ![]() 4n45S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42497.730 Da / Num. of mol.: 2 / Mutation: V77Q, N153Y, A286K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Gene: thlA, thl, CA_C2873 / Plasmid: pET30a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG 3350, K-citrate, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2011 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23985 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 34051 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 34.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 10.4 / Rejects: 0 / % possible all: 99.5 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4N45 Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1531 / FOM work R set: 0.8551 / SU B: 6.052 / SU ML: 0.148 / SU R Cruickshank DPI: 0.3196 / SU Rfree: 0.2187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 116.34 Å2 / Biso mean: 33.147 Å2 / Biso min: 13.32 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.295→2.354 Å / Total num. of bins used: 20
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