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- PDB-8y47: Crystal Structure of SCAB1 in complex with CKL2 -

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Basic information

Entry
Database: PDB / ID: 8y47
TitleCrystal Structure of SCAB1 in complex with CKL2
Components
  • Casein kinase 1-like protein 2
  • Stomatal closure-related actin-binding protein 1
KeywordsPLANT PROTEIN / cytoskeleton / plant / actin-binding / kinase
Function / homology
Function and homology information


regulation of stomatal movement / actin filament organization / actin binding / cytoskeleton / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Stomatal closure-related actin-binding protein, coiled-coil domain / Stomatal closure-related actin-binding protein, actin-binding domain / : / Stomatal closure-related actin-binding protein / Stomatal closure-related actin-binding protein, PH domain / Ig domain of plant-specific actin-binding protein / Actin-binding domain of plant-specific actin-binding protein / Coiled-coil regions of plant-specific actin-binding protein / PH domain of plant-specific actin-binding protein / : ...Stomatal closure-related actin-binding protein, coiled-coil domain / Stomatal closure-related actin-binding protein, actin-binding domain / : / Stomatal closure-related actin-binding protein / Stomatal closure-related actin-binding protein, PH domain / Ig domain of plant-specific actin-binding protein / Actin-binding domain of plant-specific actin-binding protein / Coiled-coil regions of plant-specific actin-binding protein / PH domain of plant-specific actin-binding protein / : / 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
Stomatal closure-related actin-binding protein 1 / Casein kinase 1-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, W. / Ye, K.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0570000 China
Chinese Academy of SciencesXDB37010201 China
CitationJournal: To be published
Title: Crystal Structure of SCAB1 in complex with CKL2
Authors: Zhang, W. / Ye, K.
History
DepositionJan 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stomatal closure-related actin-binding protein 1
B: Casein kinase 1-like protein 2


Theoretical massNumber of molelcules
Total (without water)26,9692
Polymers26,9692
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-10 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.378, 63.907, 89.765
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 Stomatal closure-related actin-binding protein 1


Mass: 24874.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O48791
#2: Protein/peptide Casein kinase 1-like protein 2 / Protein CASEIN KINASE I-LIKE 2


Mass: 2095.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CKL2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAI5, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.0 and 30% jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14473 / % possible obs: 98.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 27.75
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 707

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.24 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.635 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24516 708 5 %RANDOM
Rwork0.19196 ---
obs0.19456 13396 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.06 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 0 95 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191685
X-RAY DIFFRACTIONr_bond_other_d0.0020.021621
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9592269
X-RAY DIFFRACTIONr_angle_other_deg1.1233728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76123.47869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09715289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7761511
X-RAY DIFFRACTIONr_chiral_restr0.130.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
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_it2.4072.288866
X-RAY DIFFRACTIONr_mcbond_other2.4062.284865
X-RAY DIFFRACTIONr_mcangle_it3.5963.3851072
X-RAY DIFFRACTIONr_mcangle_other3.5943.391073
X-RAY DIFFRACTIONr_scbond_it3.7182.755819
X-RAY DIFFRACTIONr_scbond_other3.7162.757820
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7163.9391198
X-RAY DIFFRACTIONr_long_range_B_refined7.70418.5421796
X-RAY DIFFRACTIONr_long_range_B_other7.68218.4321778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 60 -
Rwork0.224 957 -
obs--98.83 %

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