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Yorodumi- PDB-3akl: Crystal structure of A Helicobacter pylori proinflammatory kinase CtkA -
+Open data
-Basic information
Entry | Database: PDB / ID: 3akl | ||||||
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Title | Crystal structure of A Helicobacter pylori proinflammatory kinase CtkA | ||||||
Components | Ctka | ||||||
Keywords | TRANSFERASE / protein kinase | ||||||
Function / homology | Function and homology information host cell cytosol / positive regulation of cytokine production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / non-specific serine/threonine protein kinase / phosphorylation / nucleotide binding / protein serine kinase activity / protein serine/threonine kinase activity ...host cell cytosol / positive regulation of cytokine production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / non-specific serine/threonine protein kinase / phosphorylation / nucleotide binding / protein serine kinase activity / protein serine/threonine kinase activity / host cell nucleus / magnesium ion binding / extracellular region / ATP binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Kim, D.J. / Suh, S.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Helicobacter pylori proinflammatory protein up-regulates NF-kappaB as a cell-translocating Ser/Thr kinase Authors: Kim, D.J. / Park, K.-S. / Kim, J.-H. / Yang, S.-H. / Yoon, J.Y. / Han, B.-G. / Kim, H.S. / Lee, S.J. / Jang, J.Y. / Kim, K.H. / Kim, M.J. / Song, J.-S. / Kim, H.-J. / Park, C.-M. / Lee, S.-K. ...Authors: Kim, D.J. / Park, K.-S. / Kim, J.-H. / Yang, S.-H. / Yoon, J.Y. / Han, B.-G. / Kim, H.S. / Lee, S.J. / Jang, J.Y. / Kim, K.H. / Kim, M.J. / Song, J.-S. / Kim, H.-J. / Park, C.-M. / Lee, S.-K. / Lee, B.I. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3akl.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3akl.ent.gz | 195.5 KB | Display | PDB format |
PDBx/mmJSON format | 3akl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3akl ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3akl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | AUTHOR STATED THAT THE INFORMATION ABOUT THE BIOLOGICAL ASSEMBLY WAS INDEFINITE CURRENTLY. |
-Components
#1: Protein | Mass: 37653.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: jhp_0940 / Plasmid: pET 21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) pLysS References: UniProt: Q9ZKJ5, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % / Mosaicity: 1.409 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 5.5 Details: 100 mM sodium acetate, 0.2M sodium thiocyanate, 20% (v/v) PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.9→20 Å / Num. obs: 27093 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.139 / Χ2: 3.307 / Net I/σ(I): 19.816 | ||||||||||||||||||
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Num. unique all: 1251 / Χ2: 0.92 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→19.936 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 0.1 / 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 / Bsol: 22.387 Å2 / ksol: 0.268 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.02 Å2 / Biso mean: 62.6329 Å2 / Biso min: 30.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→19.936 Å
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