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Yorodumi- PDB-6n9r: Structure of the Quorum Quenching lactonase from Parageobacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n9r | ||||||
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Title | Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL | ||||||
Components | Putative hydrolase | ||||||
Keywords | HYDROLASE / lactonase / quorum sensing / thermophile / MLL / quorum quenching / AHL | ||||||
Function / homology | Function and homology information quorum-quenching N-acyl-homoserine lactonase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Parageobacillus caldoxylosilyticus NBRC 107762 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Bergonzi, C. / Schwab, M. / Elias, M. | ||||||
Citation | Journal: Chembiochem / Year: 2019 Title: The Structural Determinants Accounting for the Broad Substrate Specificity of the Quorum Quenching Lactonase GcL. Authors: Bergonzi, C. / Schwab, M. / Naik, T. / Elias, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n9r.cif.gz | 402.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n9r.ent.gz | 326.8 KB | Display | PDB format |
PDBx/mmJSON format | 6n9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n9r_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6n9r_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6n9r_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 6n9r_validation.cif.gz | 57.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n9r ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n9r | HTTPS FTP |
-Related structure data
Related structure data | 6n9iSC 6n9qC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules APX
#1: Protein | Mass: 34378.914 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parageobacillus caldoxylosilyticus NBRC 107762 (bacteria) Gene: GCA01S_030_00190 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023DFE8 |
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-Non-polymers , 9 types, 493 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | ChemComp-PGE / | #9: Chemical | ChemComp-SO4 / #10: 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: 2.86 Å3/Da / Density % sol: 57.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Soaking in 20 mM of C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K PH range: 4.0 to 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03333 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03333 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→70.8 Å / Num. obs: 109519 / % possible obs: 99.2 % / Redundancy: 3.98 % / CC1/2: 0.999 / Rrim(I) all: 0.059 / Rsym value: 0.051 / Net I/σ(I): 15.21 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 4.07 % / Mean I/σ(I) obs: 3.32 / Num. unique obs: 16825 / CC1/2: 0.947 / Rrim(I) all: 0.48 / Rsym value: 0.419 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N9I Resolution: 1.75→70.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.959 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.115 / 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: 23.912 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→70.8 Å
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Refine LS restraints |
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