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Yorodumi- PDB-6rb3: Structural basis for recognition and ring-cleavage of the Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rb3 | |||||||||
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Title | Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqdC variant in complex with its substrate | |||||||||
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 Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / dioxygenase activity Similarity search - Function | |||||||||
Biological species | Mycobacterium abscessus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rb3.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rb3.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 6rb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rb3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6rb3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6rb3_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 6rb3_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/6rb3 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rb3 | HTTPS FTP |
-Related structure data
Related structure data | 6ra2SC 6ra3C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29746.633 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: MAB_0303 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MFK2, UniProt: A0A1M8M580*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 0.1 M tri sodium citrate pH 5.6 and 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / 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: 2.3→47.535 Å / Num. obs: 40828 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 31.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04034 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.1891 / Num. unique obs: 3981 / CC1/2: 0.905 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RA2 Resolution: 2.3→47.535 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.42 Å2 / Biso mean: 41.331 Å2 / Biso min: 17.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→47.535 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %
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