[English] 日本語
Yorodumi- PDB-5jef: Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jef | ||||||
---|---|---|---|---|---|---|---|
Title | Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in asymmetric holo state | ||||||
Components | Nitrate/nitrite sensor protein NarQ | ||||||
Keywords | TRANSFERASE / membrane protein / sensor / histidine kinase / nitrate | ||||||
Function / homology | Function and homology information cellular response to nitrate / cellular response to nitrite / histidine kinase / phosphorelay sensor kinase activity / nitrate assimilation / protein dimerization activity / signal transduction / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Popov, A. / Gordeliy, V. | ||||||
Citation | Journal: Science / Year: 2017 Title: Mechanism of transmembrane signaling by sensor histidine kinases. Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Yuzhakova, A. / Buslaev, P. / Bourenkov, G. / Grudinin, S. / Round, E. / Balandin, T. / Borshchevskiy, V. / Willbold, D. / ...Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Yuzhakova, A. / Buslaev, P. / Bourenkov, G. / Grudinin, S. / Round, E. / Balandin, T. / Borshchevskiy, V. / Willbold, D. / Leonard, G. / Buldt, G. / Popov, A. / Gordeliy, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jef.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jef.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 5jef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jef_validation.pdf.gz | 606.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jef_full_validation.pdf.gz | 612.5 KB | Display | |
Data in XML | 5jef_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5jef_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/5jef ftp://data.pdbj.org/pub/pdb/validation_reports/je/5jef | HTTPS FTP |
-Related structure data
Related structure data | 5ijiSC 5jeqC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26812.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: narQ, b2469, JW2453 / Production host: Escherichia coli (E. coli) / References: UniProt: P27896, histidine kinase #2: Chemical | ChemComp-NO3 / | #3: Chemical | ChemComp-LFA / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→52.5 Å / Num. obs: 18994 / % possible obs: 97.4 % / Redundancy: 3.34 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 7.86 |
Reflection shell | Resolution: 2.42→2.5 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.62 / % possible all: 89.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IJI Resolution: 2.42→52.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.842 / SU B: 12.06 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.419 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.42→52.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|