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- PDB-8y9o: Crystal structure of AtKAI2 in complex with KK181N1 -

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Basic information

Entry
Database: PDB / ID: 8y9o
TitleCrystal structure of AtKAI2 in complex with KK181N1
ComponentsProbable esterase KAI2
KeywordsHYDROLASE / AtKAI2 / KK181N1 / KARRIKIN-INSENSITIVE2 / plant hormone receptor
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: 1.9 Å
AuthorsWang, J.W. / Miyakawa, T. / Asami, T.
Funding support Japan, China, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05266 Japan
Japan Science and Technology Japan
Chinese Scholarship Council China
Citation
Journal: Nat Commun / Year: 2025
Title: Identification and structure-guided development of triazole urea-based selective antagonists of Arabidopsis karrikin signaling.
Authors: Wang, J. / Takahashi, I. / Kikuzato, K. / Sakai, T. / Zhu, Z. / Jiang, K. / Nakamura, H. / Nakano, T. / Tanokura, M. / Miyakawa, T. / Asami, T.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2013
Title: Smoke-derived karrikin perception by the a/b-hydrolase KAI2 from Arabidopsis
Authors: Guo, Y. / Zheng, Z. / La Clair, J.J. / Chory, J. / Noel, J.P.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable esterase KAI2
B: Probable esterase KAI2
C: Probable esterase KAI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2776
Polymers91,5923
Non-polymers6853
Water11,277626
1
A: Probable esterase KAI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7592
Polymers30,5311
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable esterase KAI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7592
Polymers30,5311
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable esterase KAI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7592
Polymers30,5311
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.314, 64.042, 114.958
Angle α, β, γ (deg.)90.000, 104.790, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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: 30530.629 Da / Num. of mol.: 3
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 (E. coli) / References: UniProt: Q9SZU7
#2: Chemical ChemComp-IB0 / (7-methyl-2,3-dihydroindol-1-yl)-(1,2,3-triazol-1-yl)methanone


Mass: 228.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H12N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.7 M sodium phosphate, pH 7.0, and 1% 1,2-butanediol
PH range: 7.0-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→43.54 Å / Num. obs: 94191 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rpim(I) all: 0.068 / Rrim(I) all: 0.128 / Rsym value: 0.108 / Net I/σ(I): 7.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4662 / CC1/2: 0.508 / Rpim(I) all: 0.488 / Rrim(I) all: 0.936 / Rsym value: 0.797 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.5419refinement
XDSdata reduction
Aimlessdata scaling
PHASER1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JYP

4jyp


Resolution: 1.9→42.35 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2747 4659 4.95 %
Rwork0.2391 89495 -
obs0.2409 94154 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 51 626 6852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00676369
X-RAY DIFFRACTIONf_angle_d0.81398673
X-RAY DIFFRACTIONf_chiral_restr0.0534984
X-RAY DIFFRACTIONf_plane_restr0.00641129
X-RAY DIFFRACTIONf_dihedral_angle_d16.02542279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.38221820.332912X-RAY DIFFRACTION99.9
1.92-1.940.34281460.3333043X-RAY DIFFRACTION99.91
1.94-1.970.35071480.30242939X-RAY DIFFRACTION99.87
1.97-1.990.30891370.30353003X-RAY DIFFRACTION99.94
1.99-2.020.30861400.27443021X-RAY DIFFRACTION99.97
2.02-2.050.31221570.2712997X-RAY DIFFRACTION99.97
2.05-2.080.34111560.2732959X-RAY DIFFRACTION99.97
2.08-2.110.28321600.26542930X-RAY DIFFRACTION99.94
2.11-2.140.32111660.25473042X-RAY DIFFRACTION99.94
2.14-2.170.30641510.26152977X-RAY DIFFRACTION99.97
2.17-2.210.31611490.2592986X-RAY DIFFRACTION99.9
2.21-2.250.29321390.26743014X-RAY DIFFRACTION99.78
2.25-2.30.29561780.25662954X-RAY DIFFRACTION99.75
2.3-2.340.3171330.25172973X-RAY DIFFRACTION99.87
2.34-2.390.30071510.24953017X-RAY DIFFRACTION99.91
2.39-2.450.27081530.23673006X-RAY DIFFRACTION99.97
2.45-2.510.28681460.23562971X-RAY DIFFRACTION99.81
2.51-2.580.28151500.23613013X-RAY DIFFRACTION99.78
2.58-2.650.31781610.24672995X-RAY DIFFRACTION99.91
2.65-2.740.28111760.2482976X-RAY DIFFRACTION99.72
2.74-2.840.28571490.2482981X-RAY DIFFRACTION99.52
2.84-2.950.28251680.24922972X-RAY DIFFRACTION99.43
2.95-3.090.26111950.22792931X-RAY DIFFRACTION99.24
3.09-3.250.2661610.23043013X-RAY DIFFRACTION99.53
3.25-3.450.2921430.23252982X-RAY DIFFRACTION98.74
3.45-3.720.23181590.22052977X-RAY DIFFRACTION98.71
3.72-4.090.24971360.20792974X-RAY DIFFRACTION97.25
4.09-4.680.22981600.20042925X-RAY DIFFRACTION96.77
4.68-5.90.23751380.22052988X-RAY DIFFRACTION97.6
5.9-42.350.2481710.23673024X-RAY DIFFRACTION96.58

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