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- PDB-8pdc: Complex of Histidine-containing phosphotransfer protein and recei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pdc | ||||||
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Title | Complex of Histidine-containing phosphotransfer protein and receiver domain of hybrid Histidine Kinase 6 from Chaetomium thermophilum | ||||||
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![]() | SIGNALING PROTEIN / Histidine-containing phosphotransferase / hybrid Histidine Kinase / Fungal / Phosphorelay / TRANSFERASE / kinase | ||||||
Function / homology | ![]() protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / phosphorylation / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paredes-Martinez, F. / Casino, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional insights underlying recognition of histidine phosphotransfer protein in fungal phosphorelay systems. Authors: Paredes-Martinez, F. / Eixeres, L. / Zamora-Caballero, S. / Casino, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.5 KB | Display | ![]() |
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PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.5 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pbwC ![]() 8phnC ![]() 8phxC ![]() 8rqgC ![]() 8rqjC ![]() 2r25S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18922.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 15849.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-BEF / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density meas: 25.66 Mg/m3 |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulphate 1 M lithium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→68.97 Å / Num. obs: 9386 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.064 / Rrim(I) all: 0.17 / Χ2: 0.99 / Net I/σ(I): 9.2 / Num. measured all: 66052 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.971 / Num. measured all: 7181 / Num. unique obs: 975 / CC1/2: 0.792 / Rpim(I) all: 0.388 / Rrim(I) all: 1.047 / Χ2: 0.97 / Net I/σ(I) obs: 2.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2R25 Resolution: 2.4→44.15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.042 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.65 / ESU R Free: 0.302 / 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: 45.106 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→44.15 Å
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Refine LS restraints |
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