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

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Basic information

Entry
Database: PDB / ID: 3akl
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase CtkA
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ctka
B: Ctka
C: Ctka
D: Ctka
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,73115
Polymers150,6154
Non-polymers2,11611
Water1,06359
1
A: Ctka
B: Ctka
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4178
Polymers75,3072
Non-polymers1,1106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-7 kcal/mol
Surface area24440 Å2
MethodPISA
2
C: Ctka
D: Ctka
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3147
Polymers75,3072
Non-polymers1,0065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-9 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.133, 74.835, 75.815
Angle α, β, γ (deg.)78.840, 71.360, 85.440
Int Tables number1
Space group name H-MP1
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.: 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 ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.11 Å3/Da / Density % sol: 41.58 % / Mosaicity: 1.409 °
Crystal growTemperature: 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

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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 315r1CCD
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: 2.9→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 shellResolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Num. unique all: 1251 / Χ2: 0.92 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
PHENIX1.5_2refinement
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2796 1316 5.03 %
Rwork0.1892 --
obs0.1938 26157 93.74 %
Solvent computationShrinkage 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 parametersBiso max: 127.02 Å2 / Biso mean: 62.6329 Å2 / Biso min: 30.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.0034 Å2-15.3757 Å2-3.0363 Å2
2--5.56 Å211.3031 Å2
3----7.5635 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9090 0 127 59 9276

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