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Open data
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Basic information
Entry | Database: PDB / ID: 4k2g | ||||||
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Title | Structure of Pseudomonas aeruginosa PvdQ bound to BRD-A33442372 | ||||||
![]() | (Acyl-homoserine lactone acylase PvdQ) x 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / amidohydrolase / bacterial protein / catalytic domain / high-throughput screening assays / molecular sequence data / oligopeptides / small molecule libraries / structure-activity relationship / 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 | ![]() ![]() | ||||||
![]() | Drake, E.J. / Wurst, J.M. / Theriault, J.R. / Munoz, B. / Gulick, A.M. | ||||||
![]() | ![]() Title: Identification of Inhibitors of PvdQ, an Enzyme Involved in the Synthesis of the Siderophore Pyoverdine. Authors: Wurst, J.M. / Drake, E.J. / Theriault, J.R. / Jewett, I.T. / VerPlank, L. / Perez, J.R. / Dandapani, S. / Palmer, M. / Moskowitz, S.M. / Schreiber, S.L. / Munoz, B. / Gulick, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.6 KB | Display | ![]() |
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PDB format | ![]() | 123.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762.5 KB | Display | ![]() |
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Full document | ![]() | 765.8 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k2fC ![]() 3l94S 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: 18592.918 Da / Num. of mol.: 1 / Fragment: alpha subunit (UNP residues 24-193) 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 / Fragment: beta subunit (UNP residues 217-762) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-1OQ / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10-15% PEG4000, 50-100 mM rubidium chloride, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 2, 2012 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15.5 Å / Num. obs: 37739 / % possible obs: 94.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.1 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3L94 Resolution: 2.3→15.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.916 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.073 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→15.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20
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