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Yorodumi- PDB-9ayt: Structure of the quorum quenching lactonase GcL bound to N-hexano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ayt | ||||||
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Title | Structure of the quorum quenching lactonase GcL bound to N-hexanoyl-L-homoserine lactone | ||||||
Components | GcL lactonase | ||||||
Keywords | HYDROLASE / quorum sensing / quorum quenching / lactonase / metalloenzyme | ||||||
Function / homology | Function and homology information quorum-quenching N-acyl-homoserine lactonase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Parageobacillus caldoxylosilyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Corbella, M. / Bravo, J.A. / Demkiv, A.O. / Calixto, A.R. / Sompiyachoke, K. / Bergonzi, C. / Kamerlin, S.C.L. / Elias, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Jacs Au / Year: 2024 Title: Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. Authors: Corbella, M. / Bravo, J. / Demkiv, A.O. / Calixto, A.R. / Sompiyachoke, K. / Bergonzi, C. / Brownless, A.R. / Elias, M.H. / Kamerlin, S.C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ayt.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ayt.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 9ayt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ayt_validation.pdf.gz | 997.9 KB | Display | wwPDB validaton report |
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Full document | 9ayt_full_validation.pdf.gz | 1006.4 KB | Display | |
Data in XML | 9ayt_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 9ayt_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/9ayt ftp://data.pdbj.org/pub/pdb/validation_reports/ay/9ayt | HTTPS FTP |
-Related structure data
Related structure data | 9b2iC 9b2jC 9b2lC 9b2nC 9b2oC 9b2pC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 2 molecules PD
#1: Protein | Mass: 34378.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parageobacillus caldoxylosilyticus (bacteria) Gene: GCA01S_030_00190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023DFE8 |
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-Non-polymers , 8 types, 250 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | ChemComp-1PE / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.33 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 1.0 - 1.25 M ammonium sulfate and 0.1 M sodium acetate pH 4.0 - 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: 1.033199 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033199 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→76.17 Å / Num. obs: 58454 / % possible obs: 99.8 % / Redundancy: 6.25 % / CC1/2: 0.996 / Net I/σ(I): 9.75 |
Reflection shell | Resolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.33 / Num. unique obs: 7610 / CC1/2: 0.853 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→76.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.44 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.558 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→76.17 Å
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