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- PDB-3uc3: The crystal structure of Snf1-related kinase 2.3 -

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Basic information

Entry
Database: PDB / ID: 3uc3
TitleThe crystal structure of Snf1-related kinase 2.3
ComponentsSerine/threonine-protein kinase SRK2I
KeywordsTRANSFERASE / SnRK2 / kinase / ABA signaling
Function / homology
Function and homology information


response to gibberellin / regulation of seed germination / response to water deprivation / response to abscisic acid / abscisic acid-activated signaling pathway / response to osmotic stress / plastid / response to salt stress / kinase activity / non-specific serine/threonine protein kinase ...response to gibberellin / regulation of seed germination / response to water deprivation / response to abscisic acid / abscisic acid-activated signaling pathway / response to osmotic stress / plastid / response to salt stress / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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. ...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
: / Serine/threonine-protein kinase SRK2I
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsZhou, X.E. / Ng, L.-M. / Soon, F.-F. / Kovach, A. / Suino-Powell, K.M. / Li, J. / Melcher, K. / Xu, H.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases.
Authors: Ng, L.M. / Soon, F.F. / Zhou, X.E. / West, G.M. / Kovach, A. / Suino-Powell, K.M. / Chalmers, M.J. / Li, J. / Yong, E.L. / Zhu, J.K. / Griffin, P.R. / Melcher, K. / Xu, H.E.
History
DepositionOct 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase SRK2I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2064
Polymers41,0291
Non-polymers1773
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.411, 75.411, 116.434
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine/threonine-protein kinase SRK2I / OST1-kinase-like 2 / Protein ATHPROKIN B / SNF1-related kinase 2.3 / SnRK2.3


Mass: 41029.484 Da / Num. of mol.: 1 / Fragment: Kinase domain / Mutation: D57A, K58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SRK2I, 41K, OSKL2, SNRK2.3, At5g66880, MUD21.14 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q39193, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG 8000, ammonium sulfate, pH 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2010
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 30761 / % possible obs: 92.8 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å11.96 Å
Translation3.5 Å11.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHASER1.3.2phasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.48 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.619 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 2193 7.1 %RANDOM
Rwork0.2124 ---
obs0.2137 28568 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 76.47 Å2 / Biso mean: 31.7002 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.56 Å20 Å2
2---1.11 Å20 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 3 143 2333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222233
X-RAY DIFFRACTIONr_bond_other_d0.0010.021560
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9673017
X-RAY DIFFRACTIONr_angle_other_deg0.76733784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7755268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61522.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71415395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1741520
X-RAY DIFFRACTIONr_chiral_restr0.0650.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_mcbond_it0.9551.51358
X-RAY DIFFRACTIONr_mcbond_other0.2351.5541
X-RAY DIFFRACTIONr_mcangle_it1.73522205
X-RAY DIFFRACTIONr_scbond_it1.9973875
X-RAY DIFFRACTIONr_scangle_it3.2674.5812
X-RAY DIFFRACTIONr_rigid_bond_restr1.18733793
X-RAY DIFFRACTIONr_sphericity_free8.5155146
X-RAY DIFFRACTIONr_sphericity_bonded4.05353747
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 147 -
Rwork0.257 2052 -
all-2199 -
obs--98.79 %

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