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- PDB-4d28: Crystal structure of the kinase domain of CIPK24/SOS2 -

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Basic information

Entry
Database: PDB / ID: 4d28
TitleCrystal structure of the kinase domain of CIPK24/SOS2
ComponentsCBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
KeywordsTRANSFERASE / SALT STRESS / SODIUM TRANSPORT / ION HOMEOSTASIS
Function / homology
Function and homology information


plant-type vacuole membrane / mitotic G2 DNA damage checkpoint signaling / response to salt stress / site of double-strand break / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CBL-interacting serine/threonine-protein kinase 24
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGonzalez-Rubio, J.M. / Chaves-Sanjuan, A. / Sanchez-Barrena, M.J. / Albert, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural Basis of the Regulatory Mechanism of the Plant Cipk Family of Protein Kinases Controlling Ion Homeostasis and Abiotic Stress
Authors: Chaves-Sanjuan, A. / Sanchez-Barrena, M.J. / Gonzalez-Rubio, J.M. / Moreno, M. / Ragel, P. / Jimenez, M. / Pardo, J.M. / Martinez-Ripoll, M. / Quintero, F.J. / Albert, A.
History
DepositionMay 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Dec 6, 2017Group: Data collection / Structure summary / Category: diffrn_source / struct / Item: _diffrn_source.pdbx_synchrotron_site / _struct.title
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
B: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
C: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
D: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24


Theoretical massNumber of molelcules
Total (without water)203,0584
Polymers203,0584
Non-polymers00
Water00
1
A: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
D: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24


Theoretical massNumber of molelcules
Total (without water)101,5292
Polymers101,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-16.4 kcal/mol
Surface area25880 Å2
MethodPISA
2
B: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24
C: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24


Theoretical massNumber of molelcules
Total (without water)101,5292
Polymers101,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-12.8 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.111, 71.353, 77.834
Angle α, β, γ (deg.)104.85, 100.32, 118.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 24 / PROTEIN SALT OVERLY SENSITIVE 2 / SNF1-RELATED KINASE 3.11 / SNRK3.11 AT5G35410


Mass: 50764.484 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PGEX4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 PLYSS
References: UniProt: Q9LDI3, non-specific serine/threonine protein kinase
Sequence detailsTHE STRUCTURE CONTAINS SOME POINT MUTATIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 20 MM TRIS PH 7.0 AND 22% PEG 4K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9786
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.3→70.2 Å / Num. obs: 15242 / % possible obs: 91 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 5.3
Reflection shellResolution: 3.3→3.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.4 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CZT

4czt


Resolution: 3.3→70.23 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.875 / SU B: 42.659 / SU ML: 0.665 / Cross valid method: THROUGHOUT / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28312 810 5 %RANDOM
Rwork0.2706 ---
obs0.2712 15242 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.668 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-1.52 Å2-2.01 Å2
2--1.24 Å2-2.3 Å2
3---3.78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→70.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8821 0 0 0 8821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199002
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.96512160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62951091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93323.658421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.823151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7581570
X-RAY DIFFRACTIONr_chiral_restr0.0730.21349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216759
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1057.0224394
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04610.5185475
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.767.074608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 58 -
Rwork0.353 1157 -
obs--90.54 %

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