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Yorodumi- PDB-7q7e: Room temperature structure of the human Serine/Threonine Kinase 1... -
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-Basic information
Entry | Database: PDB / ID: 7q7e | ||||||
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Title | Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ATP/ADP at atmospheric pressure in a sapphire capillary after high helium gas pressure release | ||||||
Components | Serine/threonine-protein kinase 17B | ||||||
Keywords | TRANSFERASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Lieske, J. / Guenther, S. / Saouane, S. / Meents, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q7e.cif.gz | 216.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q7e.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 7q7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q7e_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7q7e_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7q7e_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 7q7e_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/7q7e ftp://data.pdbj.org/pub/pdb/validation_reports/q7/7q7e | HTTPS FTP |
-Related structure data
Related structure data | 7q75C 7q76C 7q77C 7q78C 7q79C 7q7aC 7q7bC 7q7dC 7q7fC 7q7gC 7q7hC 7q7jC 7q7mC 7q7nC 7q7oC 6qf4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: STK17B, DRAK2 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % |
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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 / Pressure: 101.325 kPa |
-Data collection
Diffraction | Ambient environment: gaseous He / Ambient pressure: 101.325 kPa / Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.477 Å |
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: 2.85→48.12 Å / Num. obs: 9542 / % possible obs: 91.75 % / Redundancy: 20.8 % / Biso Wilson estimate: 69.36 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.076 / Rrim(I) all: 0.359 / Net I/σ(I): 9.44 |
Reflection shell | Resolution: 2.85→2.952 Å / Redundancy: 21.1 % / Rmerge(I) obs: 3.753 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 930 / CC1/2: 0.336 / CC star: 0.709 / Rpim(I) all: 0.812 / Rrim(I) all: 3.845 / % possible all: 92.9 |
Cell measurement | Pressure: 101.325 kPa |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QF4 Resolution: 2.85→48.12 Å / SU ML: 0.3854 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5237 / 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: 73.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.12 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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