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Yorodumi- PDB-6n9i: Structure of the Quorum Quenching lactonase from Parageobacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n9i | ||||||
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Title | Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus - free | ||||||
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: 1.6 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 | 6n9i.cif.gz | 413.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n9i.ent.gz | 336.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n9i_validation.pdf.gz | 517.3 KB | Display | wwPDB validaton report |
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Full document | 6n9i_full_validation.pdf.gz | 538.2 KB | Display | |
Data in XML | 6n9i_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 6n9i_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n9i ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n9i | HTTPS FTP |
-Related structure data
Related structure data | 6n9qC 6n9rC 2r2dS 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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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: 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 , 8 types, 705 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-PGE / #8: Chemical | #9: 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: 2.88 Å3/Da / Density % sol: 57.23 % |
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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. 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-B / Wavelength: 1.03323 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03323 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→63.93 Å / Num. obs: 602221 / % possible obs: 99.6 % / Redundancy: 4.17 % / CC1/2: 0.1 / Rrim(I) all: 0.033 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.15 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 23974 / CC1/2: 0.994 / Rrim(I) all: 0.645 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2r2d Resolution: 1.6→63.93 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.1 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.074 / 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: 33.224 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→63.93 Å
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Refine LS restraints |
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