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Open data
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Basic information
Entry | Database: PDB / ID: 1m3k | ||||||
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Title | biosynthetic thiolase, inactive C89A mutant | ||||||
![]() | Acetyl-CoA acetyltransferase | ||||||
![]() | TRANSFERASE / thiolase fold | ||||||
Function / homology | ![]() poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid beta-oxidation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kursula, P. / Ojala, J. / Lambeir, A.-M. / Wierenga, R.K. | ||||||
![]() | ![]() Title: The catalytic cycle of biosynthetic thiolase: A conformational journey of an acetyl group through four binding modes and two oxyanion holes Authors: Kursula, P. / Ojala, J. / Lambeir, A.-M. / Wierenga, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.2 KB | Display | ![]() |
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PDB format | ![]() | 252 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.5 KB | Display | ![]() |
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Full document | ![]() | 516.4 KB | Display | |
Data in XML | ![]() | 68.5 KB | Display | |
Data in CIF | ![]() | 100.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m1oC ![]() 1m1tC ![]() 1m3zC ![]() 1m4sC ![]() 1m4tC ![]() 1dluS 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: 40509.145 Da / Num. of mol.: 4 / Mutation: C89A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: lithium sulphate, ammonium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 193811 / Num. obs: 193811 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.079 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 19129 / Rsym value: 0.329 / % possible all: 56.7 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 56.7 % / Rmerge(I) obs: 0.329 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DLU Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS parameterisation / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 184714 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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