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- PDB-3akj: Crystal structure of A Helicobacter pylori proinflammatory kinase CtkA -

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Basic information

Entry
Database: PDB / ID: 3akj
TitleCrystal structure of A Helicobacter pylori proinflammatory kinase CtkA
ComponentsCtkA
KeywordsTRANSFERASE / 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
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 - #20 / Phosphorylase Kinase; domain 1 - #120 / HipA-like, C-terminal / HipA-like C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase CtkA
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKim, D.J. / Suh, S.W.
CitationJournal: 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
DepositionJul 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CtkA
B: CtkA


Theoretical massNumber of molelcules
Total (without water)75,3072
Polymers75,3072
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CtkA

B: CtkA


Theoretical massNumber of molelcules
Total (without water)75,3072
Polymers75,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1830 Å2
ΔGint-4 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.195, 56.980, 48.638
Angle α, β, γ (deg.)90.000, 93.280, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHOR STATED THAT THE INFORMATION ABOUT THE BIOLOGICAL ASSEMBLY WAS INDEFINITE CURRENTLY.

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Components

#1: Protein CtkA


Mass: 37653.688 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 100mM Tris-HCl, 1.5M AMS, 15% glycerol, pH 8.5, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPAL/PLS 4A21.0064, 1.0084, 1.0087, 0.9918
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 4, 2009
ADSC QUANTUM 315r2CCDMay 14, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00641
31.00841
41.00871
50.99181
ReflectionResolution: 2→20 Å / Num. obs: 47319

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
PHENIX1.5_2refinement
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2297 5.02 %
Rwork0.1944 --
obs0.1962 45743 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.561 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 93.96 Å2 / Biso mean: 42.5987 Å2 / Biso min: 19.69 Å2
Baniso -1Baniso -2Baniso -3
1--10.3854 Å2-0 Å2-5.5905 Å2
2--1.1388 Å20 Å2
3---9.2465 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 0 326 4814

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