[English] 日本語
Yorodumi- PDB-5w8e: The structure of a CoA-dependent acyl-homoserine lactone synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w8e | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of a CoA-dependent acyl-homoserine lactone synthase, BjaI, with the adduct of SAH and IV-CoA | ||||||
Components | Autoinducer synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / acyl-homoserine lactone / coenzyme A / BjaI | ||||||
Function / homology | ADENINE / Chem-SXZ / : Function and homology information | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Dong, S.-H. / Nair, S.K. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5w8e.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5w8e.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 5w8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/5w8e ftp://data.pdbj.org/pub/pdb/validation_reports/w8/5w8e | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25169.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: AF336_03940 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N0C224 |
---|
-Non-polymers , 5 types, 218 molecules
#2: Chemical | ChemComp-SXZ / ( |
---|---|
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-ADE / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.76 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å |
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: 1.8→25 Å / Num. obs: 41676 / % possible obs: 99.15 % / Redundancy: 6.7 % / Net I/σ(I): 13.7 |
Reflection shell | Highest resolution: 1.8 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.937 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.632 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|