[English] 日本語
Yorodumi- PDB-8biy: Citrate-free extracytoplasmic PAS domain mutant R93A of sensor hi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8biy | ||||||
---|---|---|---|---|---|---|---|
Title | Citrate-free extracytoplasmic PAS domain mutant R93A of sensor histidine kinase CitA from Geobacillus thermodenitrificans | ||||||
Components | Histidine kinase | ||||||
Keywords | SIGNALING PROTEIN / signal transduction / Geobacillus thermodenitrificans / sensor histidine kinase / CitA / sensor domain / extracytoplasmic PAS domain / R93A mutation / two-component signaling system | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / plasma membrane Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Becker, S. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published Title: Citrate-free extracytoplasmic PAS domain mutant R93A of sensor histidine kinase CitA from Geobacillus thermodenitrificans Authors: Becker, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8biy.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8biy.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 8biy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/8biy ftp://data.pdbj.org/pub/pdb/validation_reports/bi/8biy | HTTPS FTP |
---|
-Related structure data
Related structure data | 8bgbS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14040.037 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: R93A mutant Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Gene: dctS_2, GTHT12_01458 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6VSR4, histidine kinase #2: Chemical | ChemComp-CXS / #3: Chemical | #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.25 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.6 Details: 0.2M lithium sulfate, 0.9M sodium di-hydrogen phosphate, 0.6M di-potassium hydrogen phosphate, 0.1M N-cyclohexyl-3-aminopropanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→47.12 Å / Num. obs: 70580 / % possible obs: 99.1 % / Redundancy: 12.94 % / Biso Wilson estimate: 27.74 Å2 / Rrim(I) all: 0.049 / Net I/σ(I): 16.33 |
Reflection shell | Resolution: 1.61→1.64 Å / Num. unique obs: 2137 / Rrim(I) all: 0.63 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8BGB Resolution: 1.61→47.12 Å / SU ML: 0.1865 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4588 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→47.12 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|