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- PDB-7mlc: PYL10 bound to the ABA pan-antagonist 4a -

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Basic information

Entry
Database: PDB / ID: 7mlc
TitlePYL10 bound to the ABA pan-antagonist 4a
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


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
Chem-ZLA / Abscisic acid receptor PYL10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)18,4333
Polymers17,7471
Non-polymers6862
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-1 kcal/mol
Surface area8360 Å2
Unit cell
Length a, b, c (Å)59.545, 64.394, 44.597
Angle α, β, γ (deg.)90.000, 108.802, 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-430-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZLA / 1-{2-[3,5-dicyclopropyl-4-(4-{[(quinoxaline-2-carbonyl)amino]methyl}-1H-1,2,3-triazol-1-yl)phenyl]acetamido}cyclohexane-1-carboxylic acid


Mass: 593.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 46.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM tribasic ammonium citrate and 20% (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: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 15495 / % possible obs: 97 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.28 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 22.7
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 1467 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.175 / Rrim(I) all: 0.423 / % possible all: 84.8

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Processing

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

6nwb


Resolution: 1.77→42.41 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.7478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 1505 9.96 %
Rwork0.1591 13603 -
obs0.1634 15108 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.13 Å2
Refinement stepCycle: LAST / Resolution: 1.77→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 50 168 1435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871298
X-RAY DIFFRACTIONf_angle_d0.87231760
X-RAY DIFFRACTIONf_chiral_restr0.0563204
X-RAY DIFFRACTIONf_plane_restr0.0048221
X-RAY DIFFRACTIONf_dihedral_angle_d17.7331814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.830.32921160.25981057X-RAY DIFFRACTION83.61
1.83-1.890.23921250.21221180X-RAY DIFFRACTION93.15
1.89-1.970.22111370.17471223X-RAY DIFFRACTION95.84
1.97-2.060.23041400.16231228X-RAY DIFFRACTION97.51
2.06-2.170.2281370.16071247X-RAY DIFFRACTION98.16
2.17-2.30.21361410.16491286X-RAY DIFFRACTION98.75
2.3-2.480.2311400.16161253X-RAY DIFFRACTION99.57
2.48-2.730.21571410.1761270X-RAY DIFFRACTION99.72
2.73-3.120.19061400.16231273X-RAY DIFFRACTION99.72
3.12-3.940.19841420.14621279X-RAY DIFFRACTION99.93
3.94-42.410.1741460.14361307X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -10.0174222345 Å / Origin y: -4.21542671743 Å / Origin z: 7.46642439494 Å
111213212223313233
T0.158877777339 Å2-0.00558484886688 Å20.0011271643768 Å2-0.190323214454 Å20.00753059715237 Å2--0.153848338771 Å2
L1.6697085895 °20.587984881284 °2-0.170861024981 °2-1.91132217328 °20.0144001640637 °2--1.38535690078 °2
S-0.00996896499982 Å °-0.0915182144837 Å °-0.180555070685 Å °-0.0486021994957 Å °-0.00317729612834 Å °0.0253452620526 Å °-0.00380254061495 Å °-0.145032906769 Å °0.0115791626013 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 25 through 180)

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