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- PDB-6ra3: Structural basis for recognition and ring-cleavage of the Pseudom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ra3 | |||||||||
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Title | Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC in complex with its product | |||||||||
![]() | Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase) | |||||||||
![]() | HYDROLASE / dioxygenase / alpha/beta hydrolase fold / catalytic triad / quorum sensing / Pseudomonas quinolone signal / Pseudomonas aeruginosa | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wullich, S. / Kobus, S. / Smits, S.H. / Fetzner, S. | |||||||||
![]() | ![]() Title: Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqdC, a mycobacterial dioxygenase of the alpha / beta-hydrolase fold family. Authors: Wullich, S.C. / Kobus, S. / Wienhold, M. / Hennecke, U. / Smits, S.H.J. / Fetzner, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.6 KB | Display | ![]() |
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PDB format | ![]() | 250 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 718.9 KB | Display | ![]() |
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Full document | ![]() | 725.4 KB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 53.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ra2C ![]() 6rb3C ![]() 2wj3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29797.703 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SAMEA2070698_02780, SAMEA2161603_04096, SAMEA2275805_05965 Production host: ![]() ![]() #2: Chemical | ChemComp-JWH / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.10 to 0.15 M magnesium chloride, 0.1 M sodium chloride, 0.1 M MES pH 6.5 and 30 to 40 % PEG 400 at 12C. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Jul 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.086 Å / Num. obs: 60826 / % possible obs: 99.96 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09956 / Net I/σ(I): 18.83 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.6858 / Num. unique obs: 5937 / CC1/2: 0.922 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WJ3 Resolution: 2→48.086 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.37 Å2 / Biso mean: 38.9548 Å2 / Biso min: 9.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→48.086 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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