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Yorodumi- PDB-4tl0: Crystal structure of death-associated protein kinase 1 with a cru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tl0 | ||||||
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Title | Crystal structure of death-associated protein kinase 1 with a crucial phosphomimicking mutation | ||||||
Components | Death-associated protein kinase 1 | ||||||
Keywords | TRANSFERASE / kinase / death-associated / Calmodulin binding / activation mutant / phosphomimicking mutant | ||||||
Function / homology | Function and homology information cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / regulation of autophagy / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / postsynaptic density / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Temmerman, K. / Simon, B. / Wilmanns, M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of death-associated protein kinase 1 with a crucial phosphomimicking mutation Authors: Temmerman, K. / Simon, B. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tl0.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tl0.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 4tl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tl0_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 4tl0_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 4tl0_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 4tl0_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/4tl0 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/4tl0 | HTTPS FTP |
-Related structure data
Related structure data | 2w4kS 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: 38650.289 Da / Num. of mol.: 1 / Fragment: UNP residues 1-334 / Mutation: S289E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P53355, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.15 ammonium sulfate, 0.1M TRIS, pH 8.0, 15%(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.07106 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07106 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→63.539 Å / Num. all: 12440 / Num. obs: 12440 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.191 / Rsym value: 0.184 / Net I/av σ(I): 2.744 / Net I/σ(I): 11.3 / Num. measured all: 159710 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2W4K Resolution: 2.7→63.539 Å / FOM work R set: 0.8584 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.74 / 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 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.49 Å2 / Biso mean: 45.71 Å2 / Biso min: 10.44 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→63.539 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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