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- PDB-4czt: Crystal structure of the kinase domain of CIPK23 -

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Basic information

Entry
Database: PDB / ID: 4czt
TitleCrystal structure of the kinase domain of CIPK23
ComponentsCBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
KeywordsTRANSFERASE / POTASSIUM TRANSPORT / SNRK3
Function / homology
Function and homology information


stomatal movement / regulation of stomatal movement / response to water deprivation / plastid / potassium ion import across plasma membrane / potassium channel activity / response to nutrient / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity ...stomatal movement / regulation of stomatal movement / response to water deprivation / plastid / potassium ion import across plasma membrane / potassium channel activity / response to nutrient / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 23
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChaves-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
DepositionApr 22, 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 6, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
B: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
C: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
D: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,58732
Polymers207,2664
Non-polymers6,32128
Water10,611589
1
A: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
C: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,53416
Polymers103,6332
Non-polymers2,90114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-147.8 kcal/mol
Surface area25730 Å2
MethodPISA
2
B: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
D: CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,05316
Polymers103,6332
Non-polymers3,42014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-133.9 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.250, 91.460, 207.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CBL-INTERACTING SERINE/THREONINE-PROTEIN KINASE 23 / PROTEIN LOW-K(+)-SENSITIVE 1 / SNF1-RELATED KINASE 3.23 / SOS 2-LIKE PROTEIN KINASE PKS17 / SNRK3.23 AT1G30270


Mass: 51816.375 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, RESIDUES 24-482
Source method: isolated from a genetically manipulated source
Details: RESIDUES 19 TO 23 DO NOT CORRESPOND TO SNRK3. 23 AT1G30270 RESIDUES. THESE RESIDUES COMES FROM THE PGEX4T2 EXPRESSION VECTOR.
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q93VD3, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 19 TO 23 DO NOT CORRESPOND TO SNRK3.23 AT1G30270 RESIDUES. THESE RESIDUES COMES FROM THE ...RESIDUES 19 TO 23 DO NOT CORRESPOND TO SNRK3.23 AT1G30270 RESIDUES. THESE RESIDUES COMES FROM THE PGEX4T2 EXPRESION VECTOR.

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growMethod: microbatch
Details: 16 MM CHAPS 0.1 M HEPES PH 7.5, 3.5 M AMMONIUM SULFATE AS PRECIPITANT MIXED WITH THE PROTEIN AT 14 MG/ML USING MICROBATCH METHOD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→59.3 Å / Num. obs: 61816 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 13.2 % / Biso Wilson estimate: 32.88 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4J

3h4j


Resolution: 2.3→59.262 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 3133 5.1 %
Rwork0.1759 --
obs0.1789 61805 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→59.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 399 589 10272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099906
X-RAY DIFFRACTIONf_angle_d1.12213424
X-RAY DIFFRACTIONf_dihedral_angle_d14.53821
X-RAY DIFFRACTIONf_chiral_restr0.0471510
X-RAY DIFFRACTIONf_plane_restr0.0051647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33590.28811690.22852632X-RAY DIFFRACTION100
2.3359-2.37420.29271440.21932594X-RAY DIFFRACTION100
2.3742-2.41520.28491220.20962646X-RAY DIFFRACTION100
2.4152-2.45910.29491250.20812612X-RAY DIFFRACTION99
2.4591-2.50640.27961380.21332642X-RAY DIFFRACTION99
2.5064-2.55760.29621350.20642641X-RAY DIFFRACTION100
2.5576-2.61320.26121340.19242630X-RAY DIFFRACTION100
2.6132-2.6740.27641360.18972647X-RAY DIFFRACTION100
2.674-2.74080.23511290.18852623X-RAY DIFFRACTION100
2.7408-2.81490.2781600.18112620X-RAY DIFFRACTION100
2.8149-2.89780.28421390.18632679X-RAY DIFFRACTION100
2.8978-2.99130.23961540.18982630X-RAY DIFFRACTION100
2.9913-3.09820.26391430.19672646X-RAY DIFFRACTION100
3.0982-3.22220.29021300.19182690X-RAY DIFFRACTION100
3.2222-3.36890.26011600.1772635X-RAY DIFFRACTION100
3.3689-3.54650.24721250.17412701X-RAY DIFFRACTION100
3.5465-3.76860.20271470.15552669X-RAY DIFFRACTION100
3.7686-4.05960.21231310.14692694X-RAY DIFFRACTION100
4.0596-4.4680.19571480.13272700X-RAY DIFFRACTION100
4.468-5.11420.1711540.14652708X-RAY DIFFRACTION100
5.1142-6.44210.22051560.18692752X-RAY DIFFRACTION100
6.4421-59.28160.20531540.18442881X-RAY DIFFRACTION100

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