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Yorodumi- PDB-1wdl: fatty acid beta-oxidation multienzyme complex from Pseudomonas fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wdl | ||||||
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Title | fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form II (native4) | ||||||
Components |
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Keywords | LYASE / OXIDOREDUCTASE/TRANSFERASE / alpha2beta2 heterotetrameric complex / OXIDOREDUCTASE-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information 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 / 3-hydroxyacyl-CoA dehydrogenase activity ...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 / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas fragi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Ishikawa, M. / Tsuchiya, D. / Oyama, T. / Tsunaka, Y. / Morikawa, K. | ||||||
Citation | Journal: Embo J. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wdl.cif.gz | 374.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wdl.ent.gz | 307 KB | Display | PDB format |
PDBx/mmJSON format | 1wdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/1wdl ftp://data.pdbj.org/pub/pdb/validation_reports/wd/1wdl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a heterotetramer as observed in the asymmetric unit. |
-Components
#1: Protein | Mass: 77232.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fragi (bacteria) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): MIF100 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.) Pseudomonas fragi (bacteria) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): MIF100 / References: UniProt: P28790, acetyl-CoA C-acyltransferase #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG4000, MES, 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: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 5, 1998 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 27768 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.157 |
Reflection shell | Resolution: 3.5→3.72 Å / Rmerge(I) obs: 0.302 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: form I Resolution: 3.5→12 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.62 Å
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