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Yorodumi- PDB-8qcw: The crystal structure of the truncated form of Lotus japonicus ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qcw | |||||||||
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Title | The crystal structure of the truncated form of Lotus japonicus kinase 1 | |||||||||
Components | non-specific serine/threonine protein kinase | |||||||||
Keywords | TRANSFERASE / Kinase / GSK3beta-like | |||||||||
Function / homology | Function and homology information protein serine/threonine/tyrosine kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding Similarity search - Function | |||||||||
Biological species | Lotus japonicus (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Leonidas, D.D. / Solovou, T. | |||||||||
Funding support | 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qcw.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qcw.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qcw_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 8qcw_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 8qcw_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 8qcw_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/8qcw ftp://data.pdbj.org/pub/pdb/validation_reports/qc/8qcw | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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.) Lotus japonicus (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q53VM1, non-specific serine/threonine protein kinase |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
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: 0.9762 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.24 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.826 / SU B: 28.457 / SU ML: 0.51 / Cross valid method: THROUGHOUT / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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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