[English] 日本語
Yorodumi- PDB-6rgz: Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 6.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rgz | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 6.5 | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | SIGNALING PROTEIN / Histidine Kinase / Response Regulator / Phosphotransfer / Phosphatase | ||||||||||||||||||
Function / homology | Function and homology information histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / nucleotide binding / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Thermotoga maritima (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||||||||||||||
Authors | Mideros-Mora, C. / Casino, P. / Marina, A. | ||||||||||||||||||
Funding support | Spain, Ecuador, United Kingdom, 5items
| ||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases. Authors: Mideros-Mora, C. / Miguel-Romero, L. / Felipe-Ruiz, A. / Casino, P. / Marina, A. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rgz.cif.gz | 302.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rgz.ent.gz | 245.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rgz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rgz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6rgz_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 6rgz_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/6rgz ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rgz | HTTPS FTP |
-Related structure data
Related structure data | 6rfvC 6rgyC 6rh0C 6rh1C 6rh2C 6rh7C 6rh8C 3dgeS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 29378.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0853 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZV7 #2: Protein | Mass: 13913.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0468 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT9 |
---|
-Non-polymers , 5 types, 217 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.15 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1,8M HH4SO4, 0,1M citrato 6,5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97927 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→28.94 Å / Num. obs: 45694 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.999 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.35→2.43 Å / Num. unique obs: 4320 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3DGE Resolution: 2.35→28.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.514 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.257 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→28.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|