+Open data
-Basic information
Entry | Database: PDB / ID: 3l91 | ||||||
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Title | Structure of Pseudomonas aerugionsa PvdQ bound to octanoate | ||||||
Components |
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Keywords | HYDROLASE / PvdQ / pyoverdine / acylase / NTN Hydrolase / Quorum sensing / Zymogen | ||||||
Function / homology | Function and homology information acyl-homoserine-lactone acylase / : / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / quorum sensing / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / : / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / quorum sensing / 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 / FOURIER SYNTHESIS / Resolution: 1.66 Å | ||||||
Authors | Drake, E.J. / Gulick, A.M. | ||||||
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 | 3l91.cif.gz | 254.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l91.ent.gz | 198.2 KB | Display | PDB format |
PDBx/mmJSON format | 3l91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l91 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l91 | HTTPS FTP |
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-Related structure data
Related structure data | 3l94SC 3sraC 3srbC 3srcC 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: 18592.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA2385, pvdQ, qsc112 / Production host: Escherichia coli (E. coli) 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.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA2385, pvdQ, qsc112 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-OCA / | #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: 2.95 Å3/Da / Density % sol: 58.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 10-15 % PEG4000, 50-100 mM RbCl, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9782 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2009 |
Radiation | Monochromator: Horizontal focusing 5.05 asymmetric cut Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 103682 / Num. obs: 103682 / % possible obs: 93.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.65→1.75 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.1 / % possible all: 68.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3L94 Resolution: 1.66→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.343 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS used in final stages
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.171 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.657→1.699 Å / Total num. of bins used: 20
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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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