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Yorodumi- PDB-1ey3: STRUCTURE OF ENOYL-COA HYDRATASE COMPLEXED WITH THE SUBSTRATE DAC-COA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ey3 | ||||||
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Title | STRUCTURE OF ENOYL-COA HYDRATASE COMPLEXED WITH THE SUBSTRATE DAC-COA | ||||||
Components | ENOYL-COA HYDRATASE | ||||||
Keywords | LYASE / BETA-OXIDATION / CROTONASE / ENOYL-COA HYDRATASE / FATTY ACID METABOLISM / BETA-ELIMINATION / SYN-ADDITION / CONCERTED REACTION | ||||||
Function / homology | Function and homology information Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Bahnson, B.J. / Anderson, V.E. / Petsko, G.A. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an E1cb stepwise or concerted fashion. Authors: Bahnson, B.J. / Anderson, V.E. / Petsko, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ey3.cif.gz | 312.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ey3.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ey3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ey3_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1ey3_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1ey3_validation.xml.gz | 62.7 KB | Display | |
Data in CIF | 1ey3_validation.cif.gz | 84.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1ey3 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1ey3 | HTTPS FTP |
-Related structure data
Related structure data | 1dubS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | 6-subunits (A-F) come together as a dimer of trimers, forming a homo-hexamer, which is the biologically active form. |
-Components
#1: Protein | Mass: 28079.285 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Organelle: MITOCHONDRIA / Plasmid: PET20B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P14604, enoyl-CoA hydratase #2: Chemical | ChemComp-DAK / #3: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 8% PEG 4000, 100 mM sodium acetate, 75 mM sodium phosphate, 100 mM NaCl, 3 mM sodium azide, 3.5 mM DAC-CoA, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 21, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. all: 65075 / Num. obs: 65075 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.413 / Num. unique all: 5554 / % possible all: 77.1 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 95 % |
-Processing
Software |
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Refinement | Starting model: 1dub Resolution: 2.3→35 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: protein_rep.param / Details: maximum likelihood target using amplitudes
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Refinement step | Cycle: LAST / Resolution: 2.3→35 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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