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Yorodumi- PDB-6v7x: Structure of a phage-encoded quorum sensing anti-activator, Aqs1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v7x | ||||||
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Title | Structure of a phage-encoded quorum sensing anti-activator, Aqs1 bound to LasR | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/Viral protein / Prophage protein / VIRAL PROTEIN / DNA BINDING PROTEIN-Viral protein complex | ||||||
Function / homology | Function and homology information positive regulation of elastin biosynthetic process / regulation of elastin catabolic process / quorum sensing / DNA-binding transcription activator activity / protein-DNA complex / regulation of gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...positive regulation of elastin biosynthetic process / regulation of elastin catabolic process / quorum sensing / DNA-binding transcription activator activity / protein-DNA complex / regulation of gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Pseudomonas virus DMS3 Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Shah, M. / Moraes, T.F. / Maxwell, K.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Mol.Cell / Year: 2021 Title: A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Authors: Shah, M. / Taylor, V.L. / Bona, D. / Tsao, Y. / Stanley, S.Y. / Pimentel-Elardo, S.M. / McCallum, M. / Bondy-Denomy, J. / Howell, P.L. / Nodwell, J.R. / Davidson, A.R. / Moraes, T.F. / Maxwell, K.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v7x.cif.gz | 176.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v7x.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/6v7x ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v7x | HTTPS FTP |
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-Related structure data
Related structure data | 6v7uC 6v7vC 6v7wC 3ix3S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7649.417 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas virus DMS3 / Gene: DMS3-3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0SML3 #2: Protein | | Mass: 26647.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: lasR, PA14_45960 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H2Z901, UniProt: P25084*PLUS #3: Chemical | ChemComp-OHN / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.34 Å3/Da / Density % sol: 66.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6M ammonium sulfate, 0.1M MES NAOH, pH 6.5 and 10% Dioxane |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→73.92 Å / Num. obs: 13116 / % possible obs: 99.88 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 31.89 |
Reflection shell | Resolution: 2.9001→3.0038 Å / Num. unique obs: 24035 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IX3 Resolution: 2.9→73.92 Å / SU ML: 0.4565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2082
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→73.92 Å
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Refine LS restraints |
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LS refinement shell |
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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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