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- PDB-8zvn: AtKAI2 (+)-6'-carba-dMGer complex -

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Basic information

Entry
Database: PDB / ID: 8zvn
TitleAtKAI2 (+)-6'-carba-dMGer complex
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: 2.08 Å
AuthorsTakegamie, K. / Kushihara, R. / 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)31,2786
Polymers30,6111
Non-polymers6685
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-12 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.320, 55.970, 53.190
Angle α, β, γ (deg.)90.000, 98.910, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21A-573-

HOH

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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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1L2E / (2~{S})-2-[(2-nitro-4-phenyl-phenyl)methyl]-2~{H}-furan-5-one


Mass: 295.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
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: 0.72 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 2.08→47.11 Å / Num. obs: 15371 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.21 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.89
Reflection shellResolution: 2.08→2.21 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.64 / Num. unique obs: 2470

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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: 2.08→36.46 Å / SU ML: 0.2255 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 25.9807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 2969 9.94 %
Rwork0.1602 26899 -
obs0.1668 15359 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.76 Å2
Refinement stepCycle: LAST / Resolution: 2.08→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 45 178 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732277
X-RAY DIFFRACTIONf_angle_d0.83673104
X-RAY DIFFRACTIONf_chiral_restr0.0577344
X-RAY DIFFRACTIONf_plane_restr0.006407
X-RAY DIFFRACTIONf_dihedral_angle_d7.9001320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.110.36811320.29891245X-RAY DIFFRACTION94.64
2.11-2.150.32741430.24631304X-RAY DIFFRACTION99.52
2.15-2.190.29031380.23071271X-RAY DIFFRACTION99.86
2.19-2.230.27711430.21011285X-RAY DIFFRACTION99.86
2.23-2.280.29721470.20571301X-RAY DIFFRACTION99.66
2.28-2.330.31911420.18871289X-RAY DIFFRACTION99.38
2.33-2.380.24371460.18561298X-RAY DIFFRACTION99.72
2.38-2.440.23071380.17461283X-RAY DIFFRACTION99.44
2.44-2.510.2621490.17691293X-RAY DIFFRACTION99.72
2.51-2.580.28371410.16971282X-RAY DIFFRACTION99.16
2.58-2.660.23181420.17971292X-RAY DIFFRACTION99.24
2.66-2.760.28891440.18841290X-RAY DIFFRACTION98.69
2.76-2.870.23631410.1711274X-RAY DIFFRACTION98.68
2.87-30.24511400.17361265X-RAY DIFFRACTION98.39
3-3.160.22181380.16461275X-RAY DIFFRACTION97.58
3.16-3.350.25441340.14391219X-RAY DIFFRACTION95.28
3.35-3.610.171430.13671315X-RAY DIFFRACTION99.86
3.61-3.980.16981410.12851302X-RAY DIFFRACTION100
3.98-4.550.17881450.11451283X-RAY DIFFRACTION100
4.55-5.730.19951410.13011289X-RAY DIFFRACTION98.83
5.73-36.460.19971410.14871244X-RAY DIFFRACTION95.32

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