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Yorodumi- PDB-4bl1: Crystal structure of unphosphorylated Maternal Embryonic Leucine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bl1 | |||||||||
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Title | Crystal structure of unphosphorylated Maternal Embryonic Leucine zipper Kinase (MELK) in complex with AMP-PNP | |||||||||
Components | MATERNAL EMBRYONIC LEUCINE ZIPPER KINASEMELK | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Canevari, G. / Re-Depaolini, S. / Cucchi, U. / Forte, B. / Carpinelli, P. / Bertrand, J.A. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of Unphosphorylated Maternal Embryonic Leucine Zipper Kinase Authors: Canevari, G. / Re-Depaolini, S. / Cucchi, U. / Forte, B. / Carpinelli, P. / Bertrand, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bl1.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bl1.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4bl1 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4bl1 | HTTPS FTP |
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-Related structure data
Related structure data | 1zmuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40220.539 Da / Num. of mol.: 1 / Fragment: KINASE AND UBA DOMAINS, RESIDUES 2-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-ANP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % / Description: NONE |
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Crystal grow | Details: 10% PEG 3350, 0.1M BIS-TRIS PH 6.5, 0.2M SODIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→63.81 Å / Num. obs: 11375 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZMU Resolution: 2.6→52.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R: 1.571 / ESU R Free: 0.34 / 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: 48.808 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→52.44 Å
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