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- PDB-7mld: PYL10 bound to the ABA pan-antagonist antabactin -

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Basic information

Entry
Database: PDB / ID: 7mld
TitlePYL10 bound to the ABA pan-antagonist antabactin
ComponentsAbscisic acid receptor PYL10
KeywordsPLANT PROTEIN/ANTAGONIST / PYR/PYL/RCAR / PYL10 / HORMONE RECEPTOR / PLANT PROTEIN / PLANT PROTEIN-ANTAGONIST complex
Function / homology
Function and homology information


regulation of protein serine/threonine phosphatase activity / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / antabactin / Abscisic acid receptor PYL10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPeterson, F.C. / Vaidya, A.S. / Volkman, B.F. / Cutler, S.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)1656890 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Click-to-lead design of a picomolar ABA receptor antagonist with potent activity in vivo.
Authors: Vaidya, A.S. / Peterson, F.C. / Eckhardt, J. / Xing, Z. / Park, S.Y. / Dejonghe, W. / Takeuchi, J. / Pri-Tal, O. / Faria, J. / Elzinga, D. / Volkman, B.F. / Todoroki, Y. / Mosquna, A. / ...Authors: Vaidya, A.S. / Peterson, F.C. / Eckhardt, J. / Xing, Z. / Park, S.Y. / Dejonghe, W. / Takeuchi, J. / Pri-Tal, O. / Faria, J. / Elzinga, D. / Volkman, B.F. / Todoroki, Y. / Mosquna, A. / Okamoto, M. / Cutler, S.R.
History
DepositionApr 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5503
Polymers17,7471
Non-polymers8032
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint3 kcal/mol
Surface area8350 Å2
Unit cell
Length a, b, c (Å)59.753, 64.390, 44.567
Angle α, β, γ (deg.)90.000, 109.098, 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-463-

HOH

21A-500-

HOH

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Components

#1: Protein Abscisic acid receptor PYL10 / ABI1-binding protein 8 / PYR1-like protein 10 / Regulatory components of ABA receptor 4


Mass: 17747.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL10, RCAR4, At4g27920, T13J8.30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8H1R0
#2: Chemical ChemComp-ZLG / antabactin / 1-{2-[3,5-dicyclopropyl-4-(4-{[(6-fluoroquinoline-2-carbonyl)amino]methyl}-1H-1,2,3-triazol-1-yl)phenyl]acetamido}cyclohexane-1-carboxylic acid


Mass: 610.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H35FN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM tribasic ammonium citrate and 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14845 / % possible obs: 97 % / Redundancy: 7.1 % / Biso Wilson estimate: 19.37 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Rrim(I) all: 0.055 / Net I/σ(I): 25.3
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1429 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.181 / Rrim(I) all: 0.416 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NWB

6nwb


Resolution: 1.8→42.45 Å / SU ML: 0.2245 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.9493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2056 1446 10 %
Rwork0.161 13016 -
obs0.1654 14462 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 58 201 1449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091285
X-RAY DIFFRACTIONf_angle_d0.93781749
X-RAY DIFFRACTIONf_chiral_restr0.0584204
X-RAY DIFFRACTIONf_plane_restr0.005220
X-RAY DIFFRACTIONf_dihedral_angle_d16.1987806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.35721290.31441161X-RAY DIFFRACTION86.75
1.86-1.940.27671370.18061245X-RAY DIFFRACTION93.57
1.94-2.030.21461430.1621296X-RAY DIFFRACTION96.97
2.03-2.130.21531440.15791308X-RAY DIFFRACTION97.91
2.13-2.270.19531470.15621295X-RAY DIFFRACTION98.36
2.27-2.440.20651470.15891333X-RAY DIFFRACTION98.54
2.44-2.690.22361480.17651321X-RAY DIFFRACTION99.19
2.69-3.070.19121480.1621343X-RAY DIFFRACTION99.33
3.07-3.870.18741490.15021341X-RAY DIFFRACTION99.6
3.87-42.450.18811540.14331373X-RAY DIFFRACTION99.93

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