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Yorodumi- PDB-6uue: The Se-Met Structure of the Vibrio vulnificus ToxR periplasmic domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uue | ||||||
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Title | The Se-Met Structure of the Vibrio vulnificus ToxR periplasmic domain | ||||||
Components | Transcriptional activator ToxR | ||||||
Keywords | DNA BINDING PROTEIN / ToxR / Periplasm / alpha-beta / sensor | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / membrane Similarity search - Function | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.389 Å | ||||||
Authors | Kull, F.J. / Midgett, C.R. / Swindell, R.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts. Authors: Midgett, C.R. / Swindell, R.A. / Pellegrini, M. / Jon Kull, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uue.cif.gz | 33.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uue.ent.gz | 20.4 KB | Display | PDB format |
PDBx/mmJSON format | 6uue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uue_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 6uue_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 6uue_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 6uue_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/6uue ftp://data.pdbj.org/pub/pdb/validation_reports/uu/6uue | HTTPS FTP |
-Related 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: 11742.901 Da / Num. of mol.: 1 / Fragment: periplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: toxR, CRN46_04050, D8T65_08455, FORC36_0761 / Plasmid: pETVvToxRp / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: Q9RP86 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.7 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 0.1 M Ammonium formate |
-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: 0.97934 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.389→24.78 Å / Num. obs: 16768 / % possible obs: 98.73 % / Redundancy: 12.1 % / Biso Wilson estimate: 21.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06322 / Rpim(I) all: 0.0184 / Rrim(I) all: 0.06591 / Net I/σ(I): 21.66 |
Reflection shell | Resolution: 1.389→1.439 Å / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1512 / CC1/2: 0.636 / Rpim(I) all: 0.4185 / Rrim(I) all: 1.258 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.389→24.78 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.65 Å2 / Biso mean: 27.7182 Å2 / Biso min: 15.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.389→24.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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