+Open data
-Basic information
Entry | Database: PDB / ID: 4bfm | |||||||||
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Title | The crystal structure of mouse PK38 | |||||||||
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 / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity ...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 / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / calcium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Yoo, J.H. / Cho, Y.S. / Park, S.M. / Cho, H.S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The Structures of the Kinase Domain and Uba Domain of Mpk38 Suggest the Activation Mechanism for Kinase Activity. Authors: Cho, Y.S. / Yoo, J. / Park, S. / Cho, H.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bfm.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bfm.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfm ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfm | HTTPS FTP |
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-Related structure data
Related structure data | 3zgw 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: 38740.812 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q61846, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-ANP / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.35 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 15230 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 32.24 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 35.78 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.21 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZGW 3zgw Resolution: 2.35→48.896 Å / SU ML: 0.24 / σ(F): 1.52 / Phase error: 17.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→48.896 Å
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Refine LS restraints |
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LS refinement shell |
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