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Yorodumi- PDB-5oe5: Crystal structure of the N-terminal domain of PqsA in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oe5 | ||||||
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Title | Crystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 3) | ||||||
Components | Anthranilate--CoA ligase | ||||||
Keywords | LIGASE / PQS / PqsA / Anthranilate / Anthraniloyl-AMP / Anthraniloyl-CoA / Pseudomonas Quinolone Signal / Pseudomonas aeruginosa / Quorum Sensing / Aryl-CoA ligase / ANL superfamily | ||||||
Function / homology | Function and homology information anthranilate-CoA ligase / anthranilate-CoA ligase activity / acid-thiol ligase activity / secondary metabolite biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å | ||||||
Authors | Witzgall, F. / Ewert, W. / Blankenfeldt, W. | ||||||
Citation | Journal: Chembiochem / Year: 2017 Title: Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis. Authors: Witzgall, F. / Ewert, W. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oe5.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oe5.ent.gz | 197.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oe5_validation.pdf.gz | 827.9 KB | Display | wwPDB validaton report |
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Full document | 5oe5_full_validation.pdf.gz | 832 KB | Display | |
Data in XML | 5oe5_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5oe5_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oe5 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oe5 | HTTPS FTP |
-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: 44395.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsA, PA0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X3, anthranilate-CoA ligase | ||
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#2: Chemical | ChemComp-3UK / | ||
#3: Chemical | #4: 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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 100 mM tri-sodium citrate (pH 6.3), 240 mM ammonium acetate, 28.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.74→47.24 Å / Num. obs: 39169 / % possible obs: 99.3 % / Redundancy: 12.6 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.054 / Rrim(I) all: 0.193 / Net I/σ(I): 10.2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→47.236 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.88 Å2 / Biso mean: 27.252 Å2 / Biso min: 7.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→47.236 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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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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