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- PDB-6rgy: Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rgy | ||||||||||||||||||
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Title | Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5 | ||||||||||||||||||
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![]() | SIGNALING PROTEIN / Histidine Kinase / Response Regulator / Phosphotransfer / Phosphatase | ||||||||||||||||||
Function / homology | ![]() Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor / histidine phosphotransfer kinase activity / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / nucleotide binding / identical protein binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Mideros-Mora, C. / Casino, P. / Marina, A. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.1 KB | Display | ![]() |
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PDB format | ![]() | 249 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rfvC ![]() 6rgzC ![]() 6rh0C ![]() 6rh1C ![]() 6rh2C ![]() 6rh7C ![]() 6rh8C ![]() 3dgeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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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.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_0855 / Production host: ![]() ![]() References: UniProt: R4NPW0, UniProt: Q9WZV7*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor #2: Protein | Mass: 13913.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0468 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 320 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-CIT / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.54 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1,8M HH4SO4, 0,1M citrato 7,5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.2→87.11 Å / Num. obs: 55215 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.539 / Num. unique obs: 4509 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 3DGE Resolution: 2.2→87.11 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.516 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 57.273 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→87.11 Å
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Refine LS restraints |
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