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- PDB-2wyb: The quorum quenching N-acyl homoserine lactone acylase PvdQ with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wyb | ||||||
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Title | The quorum quenching N-acyl homoserine lactone acylase PvdQ with a covalently bound dodecanoic acid | ||||||
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![]() | HYDROLASE / ZYMOGEN / PERIPLASM | ||||||
Function / homology | ![]() acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bokhove, M. / Nadal Jimenez, P. / Quax, W.J. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: The Quorum-Quenching N-Acyl Homoserine Lactone Acylase Pvdq is an Ntn-Hydrolase with an Unusual Substrate-Binding Pocket Authors: Bokhove, M. / Nadal Jimenez, P. / Quax, W.J. / Dijkstra, B.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.5 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18592.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
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#2: Protein | Mass: 60489.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-DAO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 24% PEG 6000, 100 MM BICINE PH 9.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→44.52 Å / Num. obs: 55845 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.33 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.31 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.36 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.37 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.5 Å
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Refine LS restraints |
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