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- PDB-7fdf: The E145S mutant of the regulatory domain of YeiE, a sulfite sens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fdf | ||||||
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Title | The E145S mutant of the regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from Cronobacter sakazakii (sulfate-bound form) | ||||||
![]() | LysR family transcriptional regulator | ||||||
![]() | DNA BINDING PROTEIN / LysR-type transcriptional regulator / LTTR / Cronobacter sakazakii / sulfite | ||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hong, S. / Ha, N.-C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of YeiE from Cronobacter sakazakii and the role of sulfite tolerance in gram-negative bacteria. Authors: Hong, S. / Kim, J. / Cho, E. / Na, S. / Yoo, Y.J. / Cho, Y.H. / Ryu, S. / Ha, N.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.6 KB | Display | ![]() |
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Full document | ![]() | 756.6 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7erpSC ![]() 7erqC C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23221.934 Da / Num. of mol.: 1 / Mutation: E145S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH 7.5, 0.2M MgCl2, 19% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 14880 / % possible obs: 97.1 % / Redundancy: 22.2 % / Biso Wilson estimate: 20.77 Å2 / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.083 / Net I/σ(I): 36.43 |
Reflection shell | Resolution: 2.05→2.09 Å / Mean I/σ(I) obs: 5.625 / Num. unique obs: 685 / CC1/2: 0.955 / Rpim(I) all: 0.087 / Rrim(I) all: 0.429 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ERP Resolution: 2.05→35.59 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.6095 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→35.59 Å
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Refine LS restraints |
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LS refinement shell |
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