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- PDB-5w8c: The structure of a COA-dependent acyl-homoserine lactone synthase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w8c | ||||||
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Title | The structure of a COA-dependent acyl-homoserine lactone synthase, BjaI, with MTA and isovaleryl-CoA | ||||||
![]() | Autoinducer synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / acyl-homoserine lactone / coenzyme A / BjaI | ||||||
Function / homology | Isovaleryl-coenzyme A / 5'-DEOXY-5'-METHYLTHIOADENOSINE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, S.-H. / Nair, S.K. | ||||||
![]() | ![]() Title: Molecular basis for the substrate specificity of quorum signal synthases. Authors: Dong, S.H. / Frane, N.D. / Christensen, Q.H. / Greenberg, E.P. / Nagarajan, R. / Nair, S.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 | ![]() | 69.6 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 21.5 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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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25236.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 318 molecules ![](data/chem/img/IVC.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MTA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-IVC / | ||
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#3: Chemical | ChemComp-MTA / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.46 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.0 M sodium chloride, 0.085 M HEPES, pH 7.5, 15% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 77 K / Ambient temp details: liquid nitrogen |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 24, 2014 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. obs: 38415 / % possible obs: 99.93 % / Redundancy: 11.1 % / Net I/σ(I): 25.9 |
Reflection shell | Highest resolution: 1.85 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.708 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→25 Å
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Refine LS restraints |
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