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Yorodumi- PDB-1ia9: CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ia9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (AMPPNP COMPLEX) | ||||||
Components | TRANSIENT RECEPTOR POTENTIAL-RELATED PROTEIN | ||||||
Keywords | TRANSFERASE / ALPHA/BETA / PROTEIN KINASE LIKE FOLD / ATP-GRASP FOLD | ||||||
Function / homology | Function and homology information intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / monoatomic cation transmembrane transport / necroptotic process / monoatomic cation channel activity / ruffle ...intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / monoatomic cation transmembrane transport / necroptotic process / monoatomic cation channel activity / ruffle / protein tetramerization / calcium channel activity / synaptic vesicle membrane / memory / calcium ion transport / actin binding / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yamaguchi, H. / Matsushita, M. / Nairn, A.C. / Kuriyan, J. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity. Authors: Yamaguchi, H. / Matsushita, M. / Nairn, A.C. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ia9.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ia9.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ia9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1ia9 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1ia9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32246.873 Da / Num. of mol.: 2 / Fragment: PROTEIN KINASE DOMAIN, RESIDUES 1549-1828 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: CHAK / Plasmid: PFASTBAC-HTA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q923J1, EC: 2.7.1.37 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DTT / | #5: 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: 3.27 Å3/Da / Density % sol: 62.43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, ammonium phosphate, AMPPNP, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: used macroseeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96487 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 31, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96487 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 53680 / Num. obs: 53642 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 36.404 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 6.8 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.6 / Num. unique all: 5217 / Rsym value: 18.5 / % possible all: 92.1 |
Reflection shell | *PLUS % possible obs: 92.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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