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Yorodumi- PDB-5w8a: The structure of a COA-dependent acyl-homoserine lactone synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w8a | ||||||
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Title | The structure of a COA-dependent acyl-homoserine lactone synthase, BjaI, with SAM and isopentyl-CoA | ||||||
Components | Autoinducer synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / acyl-homoserine lactone / coenzyme A / BjaI | ||||||
Function / homology | isopentyl-Coenzyme A / S-ADENOSYLMETHIONINE / : Function and homology information | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w8a.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w8a.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 5w8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w8a_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5w8a_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5w8a_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5w8a_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/5w8a ftp://data.pdbj.org/pub/pdb/validation_reports/w8/5w8a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#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 |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-A1S / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.61 Å3/Da / Density % sol: 73.29 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å |
Detector | Type: RAYONIX MX300HE / 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: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 29905 / % possible obs: 99.15 % / Redundancy: 12.4 % / Net I/σ(I): 38.1 |
Reflection shell | Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.493 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 28.018 Å2
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Refinement step | Cycle: 1 / Resolution: 2→25 Å
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Refine LS restraints |
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