+
Open data
-
Basic information
Entry | Database: PDB / ID: 4k2f | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Pseudomonas aeruginosa PvdQ bound to BRD-A08522488 | ||||||
![]() | (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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 164.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 126.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 757.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 764.6 KB | Display | |
Data in XML | ![]() | 33 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k2gC ![]() 3l94S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 | ||||
---|---|---|---|---|---|
#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-A08 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50.7 Å / Num. obs: 60638 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.99→2.1 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.2 / % possible all: 98.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3L94 Resolution: 1.99→50.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.953 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.822 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→50.69 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.99→2.045 Å / Total num. of bins used: 20
|