+Open data
-Basic information
Entry | Database: PDB / ID: 2qnj | ||||||
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Title | Kinase and Ubiquitin-associated domains of MARK3/Par-1 | ||||||
Components | MAP/microtubule affinity-regulating kinase 3 | ||||||
Keywords | TRANSFERASE / serine/threonine protein kinase / ubiquitin-associated domain / MARK / PAR-1 | ||||||
Function / homology | Function and homology information peptidyl-serine autophosphorylation / negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / tau protein binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants ...peptidyl-serine autophosphorylation / negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / tau protein binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / positive regulation of protein binding / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / extracellular exosome / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Murphy, J.M. / Ceccarelli, D.F.J. / Sicheri, F. / Pawson, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain Authors: Murphy, J.M. / Korzhnev, D.M. / Ceccarelli, D.F. / Briant, D.J. / Zarrine-Afsar, A. / Sicheri, F. / Kay, L.E. / Pawson, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qnj.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qnj.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/2qnj ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qnj | 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: 37668.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MARK3, CTAK1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 References: UniProt: P27448, 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: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M LiSO4, 100 mM HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→30 Å / Num. all: 23737 / Num. obs: 23590 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.69→2.8 Å / Redundancy: 6 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.3 / % possible all: 95.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZMU Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.927 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.967 / ESU R Free: 0.367 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.715 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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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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