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- PDB-8zvo: AtKAI2 apo structure -

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Basic information

Entry
Database: PDB / ID: 8zvo
TitleAtKAI2 apo structure
ComponentsProbable esterase KAI2
KeywordsSIGNALING PROTEIN / KARRIKIN INSENSITIVE 2
Function / homology
Function and homology information


de-etiolation / response to karrikin / photomorphogenesis / hydrolase activity / nucleus / cytosol
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsTakegamie, K. / Takeuchi, J. / Nakamura, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX21BE Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural requirements of KAI2 ligands for activation of signal transduction.
Authors: Kushihara, R. / Nakamura, A. / Takegami, K. / Seto, Y. / Kato, Y. / Dohra, H. / Ohnishi, T. / Todoroki, Y. / Takeuchi, J.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable esterase KAI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3519
Polymers30,6111
Non-polymers7418
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-16 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.700, 55.790, 52.870
Angle α, β, γ (deg.)90.000, 115.940, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Probable esterase KAI2 / Protein DWARF-14-like / Protein D14-like / Protein HYPOSENSITIVE TO LIGHT / Protein KARRIKIN INSENSITIVE 2


Mass: 30610.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KAI2, D14L, HTL, At4g37470, F6G17.120 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q9SZU7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris-HCl (pH 7.0 to 9.0) with 1.25 to 2.0 M ammonium sulfate and 12% (v/v) glycerol
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.49→47.54 Å / Num. obs: 42773 / % possible obs: 96.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.76 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.95
Reflection shellResolution: 1.49→1.58 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.45 / Num. unique obs: 12465

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JYM

4jym


Resolution: 1.49→47.54 Å / SU ML: 0.1253 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.4719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1724 2005 4.69 %
Rwork0.1465 40765 -
obs0.1477 42770 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.93 Å2
Refinement stepCycle: LAST / Resolution: 1.49→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 47 363 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652316
X-RAY DIFFRACTIONf_angle_d0.91263158
X-RAY DIFFRACTIONf_chiral_restr0.0875353
X-RAY DIFFRACTIONf_plane_restr0.0064414
X-RAY DIFFRACTIONf_dihedral_angle_d14.1581847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.2611220.2312484X-RAY DIFFRACTION84.83
1.52-1.560.21431500.17622911X-RAY DIFFRACTION97.21
1.56-1.610.18571270.16492876X-RAY DIFFRACTION97.41
1.61-1.660.20391540.16762899X-RAY DIFFRACTION97.63
1.66-1.720.21971420.18072910X-RAY DIFFRACTION97.98
1.72-1.790.20541410.15722919X-RAY DIFFRACTION97.92
1.79-1.870.16981440.14492928X-RAY DIFFRACTION98.49
1.87-1.970.17091450.13892928X-RAY DIFFRACTION98.81
1.97-2.090.16941490.14352954X-RAY DIFFRACTION98.82
2.09-2.260.15561440.1422936X-RAY DIFFRACTION99.13
2.26-2.480.18561480.14262974X-RAY DIFFRACTION99.49
2.48-2.840.18221470.14552979X-RAY DIFFRACTION99.62
2.84-3.580.15861440.13453004X-RAY DIFFRACTION99.84
3.58-47.540.14281480.13643063X-RAY DIFFRACTION99.69

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