[English] 日本語
Yorodumi- PDB-6ra3: Structural basis for recognition and ring-cleavage of the Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ra3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC in complex with its product | |||||||||
Components | Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase) | |||||||||
Keywords | HYDROLASE / dioxygenase / alpha/beta hydrolase fold / catalytic triad / quorum sensing / Pseudomonas quinolone signal / Pseudomonas aeruginosa | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Mycobacteroides abscessus subsp. abscessus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Wullich, S. / Kobus, S. / Smits, S.H. / Fetzner, S. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ra3.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ra3.ent.gz | 250 KB | Display | PDB format |
PDBx/mmJSON format | 6ra3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6ra3 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6ra3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ra2C 6rb3C 2wj3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29797.703 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus subsp. abscessus (bacteria) Gene: SAMEA2070698_02780, SAMEA2161603_04096, SAMEA2275805_05965 Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M8M580 #2: Chemical | ChemComp-JWH / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97625 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WJ3 Resolution: 2→48.086 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.42
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|