+Open data
-Basic information
Entry | Database: PDB / ID: 3src | ||||||
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Title | Structure of Pseudomonas aeruginosa PvdQ bound to NS2028 | ||||||
Components | (Acyl-homoserine lactone acylase pvdQ) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / nrps tailoring / acylase / liganded / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gulick, A.M. / Drake, E.J. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2011 Title: Structural Characterization and High-Throughput Screening of Inhibitors of PvdQ, an NTN Hydrolase Involved in Pyoverdine Synthesis. Authors: Drake, E.J. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3src.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3src.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 3src.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/3src ftp://data.pdbj.org/pub/pdb/validation_reports/sr/3src | HTTPS FTP |
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-Related structure data
Related structure data | 3l91SC 3l94C 3sraC 3srbC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 17896.076 Da / Num. of mol.: 1 / Fragment: alpha subunit (UNP residues 29-191) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2385, PA2385 PvdQ, qsc112 / Plasmid: pED485 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2385, PA2385 PvdQ, qsc112 / Plasmid: pED485 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-28N / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.94 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 24, 2010 |
Radiation | Monochromator: 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: 2→39 Å / Num. all: 63767 / Num. obs: 61883 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.7 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L91 Resolution: 2→39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.78 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.164 / ESU R Free: 0.143 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.423 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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