+Open data
-Basic information
Entry | Database: PDB / ID: 2hak | ||||||
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Title | Catalytic and ubiqutin-associated domains of MARK1/PAR-1 | ||||||
Components | Serine/threonine-protein kinase MARK1 | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / SERINE/THREONINE PROTEIN KINASE / MARK / PAR-1 / KIN1 / UBA DOMAIN | ||||||
Function / homology | Function and homology information establishment of mitochondrion localization / regulation of dendrite development / phosphatidic acid binding / tau-protein kinase / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / regulation of neuron projection development / phosphatidylserine binding / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding ...establishment of mitochondrion localization / regulation of dendrite development / phosphatidic acid binding / tau-protein kinase / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / regulation of neuron projection development / phosphatidylserine binding / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding / neuron migration / tau protein binding / Wnt signaling pathway / microtubule cytoskeleton organization / microtubule cytoskeleton / peptidyl-serine phosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of gene expression / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Marx, A. / Nugoor, C. / Mueller, J. / Panneerselvam, S. / Mandelkow, E.-M. / Mandelkow, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural variations in the catalytic and ubiquitin-associated domains of microtubule-associated protein/microtubule affinity regulating kinase (MARK) 1 and MARK2 Authors: Marx, A. / Nugoor, C. / Mueller, J. / Panneerselvam, S. / Timm, T. / Bilang, M. / Mylonas, E. / Svergun, D.I. / Mandelkow, E.-M. / Mandelkow, E. #1: Journal: Structure / Year: 2006 Title: Structure of the catalytic and ubiquitin-associated domains of the protein kinase MARK/Par-1 Authors: Panneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hak.cif.gz | 477.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hak.ent.gz | 394 KB | Display | PDB format |
PDBx/mmJSON format | 2hak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hak_validation.pdf.gz | 501.2 KB | Display | wwPDB validaton report |
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Full document | 2hak_full_validation.pdf.gz | 600.3 KB | Display | |
Data in XML | 2hak_validation.xml.gz | 93.9 KB | Display | |
Data in CIF | 2hak_validation.cif.gz | 126.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/2hak ftp://data.pdbj.org/pub/pdb/validation_reports/ha/2hak | HTTPS FTP |
-Related structure data
Related structure data | 1zmuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 37712.504 Da / Num. of mol.: 8 / Fragment: catalytic and UBA domains, residues 38-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MARK1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI References: UniProt: Q9P0L2, non-specific serine/threonine protein kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 3350, 0.2M ammonium citrate, 0.1M bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 112949 / Num. obs: 112949 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.082 / Χ2: 0.995 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5506 / Χ2: 1.069 / % possible all: 98.5 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZMU Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.522 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.325 / 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: 48.596 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.604→2.667 Å / Total num. of bins used: 20
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