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- PDB-5zai: Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Meta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zai | ||||||
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Title | Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula | ||||||
![]() | 3-hydroxypropionyl-coenzyme A dehydratase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 3-hydroxypropionyl-CoA dehydratase / 3-hydroxypropionyl-CoA dehydratase activity / fatty acid metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, D. / Kim, K.J. | ||||||
![]() | ![]() Title: Structural Insight into Substrate Specificity of 3-Hydroxypropionyl-Coenzyme A Dehydratase from Metallosphaera sedula Authors: Lee, D. / Kim, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.8 KB | Display | ![]() |
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PDB format | ![]() | 265.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 66.9 KB | Display | |
Data in CIF | ![]() | 93.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pzkS S: Starting model for refinement |
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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: 28352.863 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A4YI89, 3-hydroxypropionyl-CoA dehydratase #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10%(w/v) polyethylene glycol (PEG) 8000, 0.1M Sodium-potassium phosphate, pH 6.2, 0.2M Sodium Chloride, 10mM Ethylenediaminetetraacetic acid (EDTA) disodium salt dehydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2017 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→73.75 Å / Num. obs: 138405 / % possible obs: 98.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.359 / Num. unique obs: 12686 / Rpim(I) all: 0.202 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PZK Resolution: 1.8→25.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.129 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.76 Å2 / Biso mean: 26.948 Å2 / Biso min: 8.7 Å2
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Refinement step | Cycle: final / Resolution: 1.8→25.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.796→1.843 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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