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Open data
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Basic information
Entry | Database: PDB / ID: 6pca | ||||||
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Title | Crystal structure of beta-ketoadipyl-CoA thiolase | ||||||
![]() | Beta-ketoadipyl-CoA thiolase | ||||||
![]() | TRANSFERASE / Thiolase / aromatic pollutant catabolism / degradative enzymes | ||||||
Function / homology | ![]() 3-oxoadipyl-CoA thiolase / 3-oxoadipyl-CoA thiolase activity / acetyl-CoA C-acyltransferase activity / 3,4-dihydroxybenzoate catabolic process / phenylacetate catabolic process / fatty acid beta-oxidation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sukritee, B. / Panjikar, S. | ||||||
![]() | ![]() Title: Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase. Authors: Bhaskar, S. / Steer, D.L. / Anand, R. / Panjikar, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 322.3 KB | Display | ![]() |
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PDB format | ![]() | 257.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.3 KB | Display | ![]() |
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Full document | ![]() | 368.5 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pcbC ![]() 6pccC ![]() 6pcdC ![]() 1ulqS 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: 44446.660 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pcaF-I, PP_1377 / Production host: ![]() ![]() References: UniProt: Q88N39, acetyl-CoA C-acyltransferase, 3-oxoadipyl-CoA thiolase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.18 % / Description: Plate type |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion / Details: lithium chloride,PEG 6000,tris (pH- 7.3-8.3) / PH range: 7.3-8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→84.89 Å / Num. obs: 281317 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.55 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.104 / Net I/σ(I): 10.28 |
Reflection shell | Resolution: 1.81→1.92 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 44875 / CC1/2: 0.696 / Rrim(I) all: 0.702 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ULQ Resolution: 1.81→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.762 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.328 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→20 Å
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Refine LS restraints |
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