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Yorodumi- PDB-2br6: Crystal Structure of Quorum-Quenching N-Acyl Homoserine Lactone L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2br6 | ||||||
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Title | Crystal Structure of Quorum-Quenching N-Acyl Homoserine Lactone Lactonase | ||||||
Components | AIIA-LIKE PROTEINLactonase | ||||||
Keywords | HYDROLASE / QUORUM SENSING / QUORUM-QUENCHING ENZYME / ACYL-HSL LACTONASE / ACYL-HOMOSERINE | ||||||
Function / homology | Function and homology information acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS THURINGIENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kim, M.H. / Choi, W.C. / Kang, H.O. / Kang, B.S. / Kim, K.J. / Derewenda, Z.S. / Lee, J.K. / Oh, T.K. / Lee, C.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: The Molecular Structure and Catalytic Mechanism of a Quorum-Quenching N-Acyl-L-Homoserine Lactone Hydrolase. Authors: Kim, M.H. / Choi, W.C. / Kang, H.O. / Lee, J.S. / Kang, B.S. / Kim, K.J. / Derewenda, Z.S. / Oh, T.K. / Lee, C.H. / Lee, J.K. #1: Journal: Biochim.Biophys.Acta / Year: 2005 Title: Crystallization and Preliminary Crystallographic Analysis of Bacillus Thuringiensis Ahl-Lactonase. Authors: Kim, M.H. / Kang, H.O. / Kang, B.S. / Kim, K.J. / Choi, W.C. / Oh, T.K. / Lee, C.H. / Lee, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2br6.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2br6.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 2br6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/2br6 ftp://data.pdbj.org/pub/pdb/validation_reports/br/2br6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28496.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Plasmid: PMAL-HIS-PARALLEL1/AIIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI XL1-BLUE / References: UniProt: Q7B8C3, UniProt: P0CJ63*PLUS | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-HSL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % |
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Crystal grow | pH: 7.8 Details: 0.1 M TRIS-HCL(PH 7.8), 30% PEG 4000,0.2 M MGCL2, 2 MM HOMOSERINE LACTONE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.0781 |
Detector | Detector: CCD / Date: Feb 20, 2005 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44 Å / Num. obs: 23923 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.1 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.73 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.118 / 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: 19.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→44 Å
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Refine LS restraints |
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