+Open data
-Basic information
Entry | Database: PDB / ID: 5ubl | ||||||
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Title | A circularly permuted version of PvdQ (cpPvdQ) | ||||||
Components | Acyl-homoserine lactone acylase PvdQ | ||||||
Keywords | HYDROLASE / cpPVDQ / PVDQ / pyoverdine biosynthesis pathway / (Ntn) hydrolase | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Wu, R. / Mascarenhas, R. / Catlin, D. / Clevenger, K. / Fast, W. / Liu, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Circular Permutation Reveals a Chromophore Precursor Binding Pocket of the Siderophore Tailoring Enzyme PvdQ Authors: Clevenger, K. / Mascarenhas, R. / Catlin, D. / Wu, R. / Fast, W. / Liu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ubl.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ubl.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ubl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubl ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubl | HTTPS FTP |
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-Related 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: 81006.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pvdQ / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q9I194, acyl-homoserine-lactone acylase |
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#2: 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: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.05 M Hepes (pH 7.5), 80 mM RbCl, 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 271 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Jun 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→67.9 Å / Num. obs: 88115 / % possible obs: 98 % / Redundancy: 5.5 % / Net I/σ(I): 8 |
-Processing
Software |
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Refinement | Resolution: 1.8→50.99 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50.99 Å
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Refine LS restraints |
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LS refinement shell |
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