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Yorodumi- PDB-6cgz: Structure of the Quorum Quenching lactonase from Alicyclobacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cgz | ||||||
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Title | Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to C6-AHL | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / lactonase / acyl homoserine lactone hydrolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Alicyclobacillus acidoterrestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Bergonzi, C. / Schwab, M. / Naik, T. / Daude, D. / Chabriere, E. / Elias, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties. Authors: Bergonzi, C. / Schwab, M. / Naik, T. / Daude, D. / Chabriere, E. / Elias, M. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: The quorum-quenching lactonase from Alicyclobacter acidoterrestris: purification, kinetic characterization, crystallization and crystallographic analysis. Authors: Bergonzi, C. / Schwab, M. / Chabriere, E. / Elias, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cgz.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cgz.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 6cgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/6cgz ftp://data.pdbj.org/pub/pdb/validation_reports/cg/6cgz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 32078.346 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidoterrestris (strain ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B) (bacteria) Strain: ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B Gene: N007_09425 / Production host: Escherichia coli (E. coli) / References: UniProt: T0BMH6 |
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-Non-polymers , 6 types, 614 molecules
#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PG4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Purified and concentrated AaL samples (10 mg ml) were subjected to crystallization trialsCrystals appeared after 1 d at 292 K in a condition consisting of 0.45M ammonium chloride, 16% ...Details: Purified and concentrated AaL samples (10 mg ml) were subjected to crystallization trialsCrystals appeared after 1 d at 292 K in a condition consisting of 0.45M ammonium chloride, 16% polyethylene glycol 3350. Seeding was performed as described previously (PMID: 28777091) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03312 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03312 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→57.31 Å / Num. obs: 90111 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rsym value: 0.054 / Net I/σ(I): 18.27 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.3 % / Num. unique obs: 13463 / Rsym value: 0.59 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Resolution: 1.8→57.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.528 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.114 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→57.31 Å
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Refine LS restraints |
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