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Yorodumi- PDB-6ra2: Structural basis for recognition and ring-cleavage of the Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ra2 | |||||||||
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Title | Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC | |||||||||
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 | Mycobacteroides abscessus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 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 | 6ra2.cif.gz | 174 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ra2.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ra2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ra2_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
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Full document | 6ra2_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 6ra2_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 6ra2_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/6ra2 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6ra2 | HTTPS FTP |
-Related structure data
Related structure data | 6ra3C 6rb3C 2wj3S 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: 29797.703 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: MAB_0303 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MFK2, UniProt: A0A1M8M580*PLUS #2: 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: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 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. PH range: 6.2-6.8 |
-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→46.91 Å / Num. obs: 40361 / % possible obs: 99.3 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06186 / Net I/σ(I): 29.82 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.1996 / Num. unique obs: 3990 / CC1/2: 0.984 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WJ3 Resolution: 2.3→46.907 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 3.2 / Phase error: 24.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.907 Å
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Refine LS restraints |
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LS refinement shell |
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