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- PDB-4wks: n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Spec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wks | ||||||
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Title | n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the Quorum-Quenching and Siderophore Biosynthetic Enzyme PvdQ | ||||||
![]() | (Acyl-homoserine lactone acylase PvdQ) x 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / PVDQ / n-Alkylboronic Acid / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Wu, R. / Clevenger, D.K. / Fast, W. / Liu, D. | ||||||
![]() | ![]() Title: n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the Quorum-Quenching and Siderophore Biosynthetic Enzyme PvdQ. Authors: Clevenger, K.D. / Wu, R. / Liu, D. / Fast, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.9 KB | Display | ![]() |
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PDB format | ![]() | 246.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 53.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wktC ![]() 4wkuC ![]() 4wkvC ![]() 4m1jS C: citing same article ( S: Starting model for refinement |
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Similar 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: 60632.078 Da / Num. of mol.: 1 / Fragment: UNP residues 217-762 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: 17993.191 Da / Num. of mol.: 1 / Fragment: UNP residues 28-192 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9I194, acyl-homoserine-lactone acylase |
#3: Chemical | ChemComp-3QD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.84 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: Hepes (50 mM) at pH 7.5; RbCl (80 mM); PEG-4000 10% (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.6 Å / Num. obs: 119528 / % possible obs: 99.5 % / Redundancy: 3.8 % / Net I/σ(I): 12.7 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4M1J Resolution: 1.629→42.587 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.629→42.587 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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