+Open data
-Basic information
Entry | Database: PDB / ID: 9b2i | ||||||
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Title | Structure of the quorum quenching lactonase GcL G156P mutant | ||||||
Components | quorum-quenching N-acyl-homoserine 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: 2.35 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 | 9b2i.cif.gz | 200.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b2i.ent.gz | 159.4 KB | Display | PDB format |
PDBx/mmJSON format | 9b2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b2i_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 9b2i_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 9b2i_validation.xml.gz | 42.6 KB | Display | |
Data in CIF | 9b2i_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/9b2i ftp://data.pdbj.org/pub/pdb/validation_reports/b2/9b2i | HTTPS FTP |
-Related structure data
Related structure data | 9aytC 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, 3 molecules ABC
#1: Protein | Mass: 34418.977 Da / Num. of mol.: 3 / Mutation: G156P 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, quorum-quenching N-acyl-homoserine lactonase |
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-Non-polymers , 8 types, 399 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / | #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: 2.78 Å3/Da / Density % sol: 55.68 % |
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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: 0.99184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99184 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→64.83 Å / Num. obs: 45944 / % possible obs: 97.6 % / Redundancy: 4.01 % / CC1/2: 0.998 / Net I/σ(I): 13.23 |
Reflection shell | Resolution: 2.35→2.45 Å / Mean I/σ(I) obs: 2.46 / Num. unique obs: 5396 / CC1/2: 0.872 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→64.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.99 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.224 / 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: 52.157 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→64.12 Å
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