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- PDB-8qcw: The crystal structure of the truncated form of Lotus japonicus ki... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qcw | |||||||||
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Title | The crystal structure of the truncated form of Lotus japonicus kinase 1 | |||||||||
![]() | non-specific serine/threonine protein kinase![]() | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() protein serine/threonine/tyrosine kinase activity / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leonidas, D.D. / Solovou, T. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Biochemical and Structural Studies of LjSK1, a Lotus japonicus GSK3 beta /SHAGGY-like Kinase, Reveal Its Functional Role. Authors: Solovou, T.G.A. / Stravodimos, G. / Papadopoulos, G.E. / Skamnaki, V.T. / Papadopoulou, K. / Leonidas, D.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 63.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 52776.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q53VM1, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % / Description: thin plates |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 27 mM NaNO3, 27 mM Na2HPO4, 27 mM ammonium sulfate, 0.1 M MES, 12% (v/v) PEG 500 MME & 6% (v/v) PEG 20000 |
-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: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→43.24 Å / Num. obs: 8837 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 50 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1395 / CC1/2: 0.359 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.633 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→43.24 Å
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Refine LS restraints |
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