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- PDB-7q7d: Room temperature structure of the human Serine/Threonine Kinase 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7q7d | ||||||
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Title | Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ATP/ADP at 111 MPa helium gas pressure in a sapphire capillary | ||||||
![]() | Serine/threonine-protein kinase 17B | ||||||
![]() | TRANSFERASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature | ||||||
Function / homology | ![]() positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation ...positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lieske, J. / Guenther, S. / Saouane, S. / Meents, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Fixed-target high-pressure macromolecular crystallography Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / Gabdulkhakov, A.G. / Selikhanov, G.K. / Chapman, H.N. / Meents, 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 | ![]() | 216.7 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q75C ![]() 7q76C ![]() 7q77C ![]() 7q78C ![]() 7q79C ![]() 7q7aC ![]() 7q7bC ![]() 7q7eC ![]() 7q7fC ![]() 7q7gC ![]() 7q7hC ![]() 7q7jC ![]() 7q7mC ![]() 7q7nC ![]() 7q7oC ![]() 6qf4S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 37327.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O94768, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 295 K / Method: batch mode Details: 20 mg/ml protein in 25 mM HEPES pH 7.5, 500 mM NaCl, 0.5 mM TCEP was mixed 1:1.5 with precipitant solution (0.1 M HEPES 6.5, 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium ...Details: 20 mg/ml protein in 25 mM HEPES pH 7.5, 500 mM NaCl, 0.5 mM TCEP was mixed 1:1.5 with precipitant solution (0.1 M HEPES 6.5, 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin). Batch grown crystals were subsequently mixed 1:1 with 100 mM ATP/50 mM magnesium chloride in DRAK2 crystallization buffer and incubated for half an hour. PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Sep 30, 2019 |
Diffraction measurement | Specimen support: sapphire capillary |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.477 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.46 Å / Num. obs: 12947 / % possible obs: 96.68 % / Redundancy: 25.8 % / Biso Wilson estimate: 62.73 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.042 / Rrim(I) all: 0.218 / Net I/σ(I): 13.03 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 24.1 % / Rmerge(I) obs: 2.875 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 1181 / CC1/2: 0.446 / CC star: 0.785 / Rpim(I) all: 0.584 / Rrim(I) all: 2.937 / % possible all: 89.2 |
Cell measurement | Pressure: 111000 kPa |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QF4 Resolution: 2.6→39.46 Å / SU ML: 0.2968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5288 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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