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- PDB-8qcw: The crystal structure of the truncated form of Lotus japonicus ki... -

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Basic information

Entry
Database: PDB / ID: 8qcw
TitleThe crystal structure of the truncated form of Lotus japonicus kinase 1
Componentsnon-specific serine/threonine protein kinase
KeywordsTRANSFERASE / Kinase / GSK3beta-like
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / signal transduction / ATP binding / cytoplasm
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / 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
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLeonidas, D.D. / Solovou, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Biochemical and Structural Studies of LjSK1, a Lotus japonicus GSK3 beta /SHAGGY-like Kinase, Reveal Its Functional Role.
Authors: Solovou, T.G.A. / Stravodimos, G. / Papadopoulos, G.E. / Skamnaki, V.T. / Papadopoulou, K. / Leonidas, D.D.
History
DepositionAug 28, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 21, 2024ID: 8AHP
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 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: non-specific serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)52,7761
Polymers52,7761
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.318, 69.323, 99.641
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 non-specific serine/threonine protein kinase


Mass: 52776.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q53VM1, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.56 % / Description: thin plates
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27 mM NaNO3, 27 mM Na2HPO4, 27 mM ammonium sulfate, 0.1 M MES, 12% (v/v) PEG 500 MME & 6% (v/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→43.24 Å / Num. obs: 8837 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 50 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.7
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1395 / CC1/2: 0.359 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.24 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.826 / SU B: 28.457 / SU ML: 0.51 / Cross valid method: THROUGHOUT / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3104 882 10 %RANDOM
Rwork0.24367 ---
obs0.2502 7936 98.76 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.09 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.9→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 0 8 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0122952
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162819
X-RAY DIFFRACTIONr_angle_refined_deg0.8281.6714010
X-RAY DIFFRACTIONr_angle_other_deg0.2741.5736505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.228518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81710502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
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_it2.1125.6811430
X-RAY DIFFRACTIONr_mcbond_other2.1125.6811430
X-RAY DIFFRACTIONr_mcangle_it3.70110.2171778
X-RAY DIFFRACTIONr_mcangle_other3.710.2161779
X-RAY DIFFRACTIONr_scbond_it1.6355.8921522
X-RAY DIFFRACTIONr_scbond_other1.6085.8891518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.93510.7672233
X-RAY DIFFRACTIONr_long_range_B_refined7.89966.6411879
X-RAY DIFFRACTIONr_long_range_B_other7.89866.6411879
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 71 -
Rwork0.365 550 -
obs--99.2 %

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