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Yorodumi- PDB-6p7r: Crystal structure of unsaturated fatty acid bound wild-type ToxT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p7r | ||||||
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Title | Crystal structure of unsaturated fatty acid bound wild-type ToxT from Vibrio cholerae strain SCE256 | ||||||
Components | Toxin co-regulated pilus virulence regulatory protein | ||||||
Keywords | DNA BINDING PROTEIN / AraC / XylS / virulence regulation / cholerae | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Cruite, J.T. / Kull, F.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2019 Title: Structural basis for virulence regulation inVibrio choleraeby unsaturated fatty acid components of bile. Authors: Cruite, J.T. / Kovacikova, G. / Clark, K.A. / Woodbrey, A.K. / Skorupski, K. / Kull, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p7r.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p7r.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7r ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7r | HTTPS FTP |
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-Related structure data
Related structure data | 6p7tC 6pb9C 3gbgS 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: 32221.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F5Q9 |
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#2: Chemical | ChemComp-PAM / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.3 Å / Num. obs: 26994 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05351 / Rpim(I) all: 0.02976 / Rrim(I) all: 0.06146 / Net I/av σ(I): 13.73 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5168 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 1786 / CC1/2: 0.78 / Rpim(I) all: 0.2947 / Rrim(I) all: 0.5974 / % possible all: 99.92 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GBG Resolution: 1.8→28.3 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.05 Å2 / Biso mean: 46.11 Å2 / Biso min: 15.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→28.3 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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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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