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Yorodumi- PDB-7l5f: Crystal Structure of N-(2-oxocyclobutyl) decanamide Bound AiiA-Co -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l5f | ||||||
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Title | Crystal Structure of N-(2-oxocyclobutyl) decanamide Bound AiiA-Co | ||||||
Components | N-acyl homoserine lactonase AiiA | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / AiiA-Co / lactonase / quorum-quenching / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis subsp. kurstaki (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Mascarenhas, R.N. / Liu, D. | ||||||
Citation | Journal: Acs Omega / Year: 2021 Title: Cyclobutanone Inhibitor of Cobalt-Functionalized Metallo-gamma-Lactonase AiiA with Cyclobutanone Ring Opening in the Active Site. Authors: Reidl, C.T. / Mascarenhas, R. / Mohammad, T.S.H. / Lutz Jr., M.R. / Thomas, P.W. / Fast, W. / Liu, D. / Becker, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l5f.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l5f.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 7l5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l5f_validation.pdf.gz | 658.1 KB | Display | wwPDB validaton report |
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Full document | 7l5f_full_validation.pdf.gz | 660 KB | Display | |
Data in XML | 7l5f_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 7l5f_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/7l5f ftp://data.pdbj.org/pub/pdb/validation_reports/l5/7l5f | HTTPS FTP |
-Related structure data
Related structure data | 2a7mS 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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-Components
#1: Protein | Mass: 28250.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis subsp. kurstaki (bacteria) Gene: aiiA / Production host: Escherichia coli (E. coli) References: UniProt: P0CJ63, quorum-quenching N-acyl-homoserine lactonase | ||||||
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#2: Chemical | ChemComp-GOL / | ||||||
#3: Chemical | #4: Chemical | ChemComp-XNG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 160 mM MgCl2-6H20, 80 mM bis-Tris pH 8.5, 24% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 49262 / % possible obs: 98.2 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.51→1.56 Å / Num. unique obs: 2023 / CC1/2: 0.361 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A7M Resolution: 1.51→40.29 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.19 Å2 / Biso mean: 19.3407 Å2 / Biso min: 5.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.51→40.29 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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