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- PDB-1xte: crystal structure of CISK-PX domain -

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Basic information

Entry
Database: PDB / ID: 1xte
Titlecrystal structure of CISK-PX domain
ComponentsSerine/threonine-protein kinase Sgk3
KeywordsTRANSFERASE / CISK / PX domain
Function / homology
Function and homology information


Stimuli-sensing channels / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / potassium channel regulator activity / phosphatidylinositol binding / recycling endosome / cytoplasmic vesicle / molecular adaptor activity / early endosome / non-specific serine/threonine protein kinase / intracellular signal transduction ...Stimuli-sensing channels / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / potassium channel regulator activity / phosphatidylinositol binding / recycling endosome / cytoplasmic vesicle / molecular adaptor activity / early endosome / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/threonine-protein kinase Sgk3, catalytic domain / CISK, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Protein kinase, C-terminal ...Serine/threonine-protein kinase Sgk3, catalytic domain / CISK, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase Sgk3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsXing, Y. / Liu, D. / Zhang, R. / Joachimiak, A. / Songyang, Z. / Xu, W.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis of membrane targeting by the Phox homology domain of cytokine-independent survival kinase (CISK-PX)
Authors: Xing, Y. / Liu, D. / Zhang, R. / Joachimiak, A. / Songyang, Z. / Xu, W.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 14, 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: Serine/threonine-protein kinase Sgk3


Theoretical massNumber of molelcules
Total (without water)18,0231
Polymers18,0231
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.954, 74.954, 51.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Serine/threonine-protein kinase Sgk3 / CISK-PX DOMAIN / Serum/glucocorticoid regulated kinase 3 / Serum/glucocorticoid regulated kinase- ...CISK-PX DOMAIN / Serum/glucocorticoid regulated kinase 3 / Serum/glucocorticoid regulated kinase-like / Cytokine independent survival kinase


Mass: 18023.299 Da / Num. of mol.: 1
Fragment: sequence database residues 7-160: contains PX domain (residues 12-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cisk / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9ERE3, EC: 2.7.1.37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium citrate, sodium malonate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11501
21501
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97934
SYNCHROTRONAPS 19-ID20.97933
Detector
TypeIDDetectorDate
ANL-ECD1CCDAug 19, 2002
CUSTOM-MADE2CCDOct 22, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979331
ReflectionResolution: 1.6→50 Å / Num. all: 18760 / Num. obs: 18760 / % possible obs: 98.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.04 / Net I/σ(I): 34
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1855 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→42.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 791671.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1398 7.8 %RANDOM
Rwork0.187 ---
obs0.187 17839 93.8 %-
all-18760 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6644 Å2 / ksol: 0.378731 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-50 Å
Luzzati sigma a0.1 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 0 149 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it1.941.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it3.362
X-RAY DIFFRACTIONc_scangle_it4.822.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 191 7.3 %
Rwork0.219 2434 -
obs--84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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