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- PDB-1wdk: fatty acid beta-oxidation multienzyme complex from Pseudomonas fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wdk | ||||||
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Title | fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2) | ||||||
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![]() | LYASE / OXIDOREDUCTASE/TRANSFERASE / alpha2beta2 heterotetrameric complex / OXIDOREDUCTASE-TRANSFERASE COMPLEX | ||||||
Function / homology | ![]() fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / phenylacetate catabolic process ...fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / phenylacetate catabolic process / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ishikawa, M. / Tsuchiya, D. / Oyama, T. / Tsunaka, Y. / Morikawa, K. | ||||||
![]() | ![]() Title: Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex Authors: Ishikawa, M. / Tsuchiya, D. / Oyama, T. / Tsunaka, Y. / Morikawa, K. #1: Journal: Biochem.J. / Year: 1997 Title: Reconstitution, morphology and crystallization of a fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi Authors: Ishikawa, M. / Mikami, Y. / Usukura, J. / Iwasaki, H. / Shinagawa, H. / Morikawa, 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 | ![]() | 443.8 KB | Display | ![]() |
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PDB format | ![]() | 358.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 92.2 KB | Display | |
Data in CIF | ![]() | 127.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a heterotetramer as observed in the asymmetric unit. |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 77232.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28793, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase, 3-hydroxybutyryl-CoA epimerase #2: Protein | Mass: 41522.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 984 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/N8E.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/N8E.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-N8E / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG4000, MES, ZnCl2, n-octylpentaoxyethylene, NAD+, acetoacetyl-CoA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2002 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 82900 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.7 / % possible all: 80.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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