+Open data
-Basic information
Entry | Database: PDB / ID: 8jwd | ||||||
---|---|---|---|---|---|---|---|
Title | Histidine kinase QseE sensor domain of Escherichia coli O157:H7 | ||||||
Components | histidine kinase | ||||||
Keywords | TRANSFERASE / Enterohemorrhagic Escherichia coli / Two-component systems / Inner membrane protein / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Matsumoto, K. / Fukuda, Y. / Inoue, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Crystal structures of QseE and QseG: elements of a three-component system from Escherichia coli. Authors: Matsumoto, K. / Fukuda, Y. / Inoue, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jwd.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jwd.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 8jwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/8jwd ftp://data.pdbj.org/pub/pdb/validation_reports/jw/8jwd | HTTPS FTP |
---|
-Related structure data
Related structure data | 7x6fC 7x6gC 7x6hC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16528.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: qseE, C2R31_001944, HEP34_004735 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2T3SYV0, histidine kinase |
---|---|
#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 25.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.15 M sodium formate, 0.1 M HEPES pH 7.2, 18% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→43.5 Å / Num. obs: 25729 / % possible obs: 98.9 % / Redundancy: 18.9 % / Biso Wilson estimate: 12.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.015 / Rrim(I) all: 0.065 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1183 / CC1/2: 0.933 / Rpim(I) all: 0.185 / Rrim(I) all: 0.704 / % possible all: 95.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→43.5 Å / SU ML: 0.1438 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3183 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→43.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|