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- PDB-6nwb: PYL10 bound to the selective agonist hexabactin -

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Basic information

Entry
Database: PDB / ID: 6nwb
TitlePYL10 bound to the selective agonist hexabactin
ComponentsAbscisic acid receptor PYL10
KeywordsPLANT PROTEIN / PYR/PYL/RCAR / PYL10 / HORMONE RECEPTOR
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 domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L6V / Abscisic acid receptor PYL10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.003 Å
AuthorsPeterson, F.C. / Vaidya, A. / Jensen, D.R. / Volkman, B.F. / Cutler, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)12581750 United States
National Science Foundation (NSF, United States)165689 United States
CitationJournal: To Be Published
Title: PYL10 bound to the selective agonist hexabactin
Authors: Elzinga, D. / Vaidya, A.S. / Peterson, F.C. / Park, S.Y. / Volkman, B.F. / Okamoto, M. / Cutler, S.R.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,7642
Polymers17,3761
Non-polymers3891
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.910, 65.910, 65.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-374-

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: 17375.789 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) / Strain (production host): BL21(DE3) / References: UniProt: Q8H1R0
#2: Chemical ChemComp-L6V / N-{[(4-cyanophenyl)methyl]sulfonyl}-1-(thiophen-3-yl)cyclohexane-1-carboxamide


Mass: 388.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6
Details: Well solution was composed of 0.1 M MMT buffer pH 6.0 plus 25% w/v PEG 1500. Crystals were flash frozen in well solution plus 15% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10999 / % possible obs: 96.3 % / Redundancy: 20.8 % / Biso Wilson estimate: 32.24 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.06 / Rrim(I) all: 0.08 / Net I/σ(I): 37.1
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 16.6 / Num. unique obs: 435 / Rpim(I) all: 0.018 / Rrim(I) all: 0.265 / % possible all: 78.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.77 Å42.9 Å
Translation5.77 Å42.9 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RT0

3rt0


Resolution: 2.003→42.898 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.65
RfactorNum. reflection% reflection
Rfree0.2242 1095 9.96 %
Rwork0.1736 --
obs0.1788 10999 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.95 Å2 / Biso mean: 40.1925 Å2 / Biso min: 16.86 Å2
Refinement stepCycle: final / Resolution: 2.003→42.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 26 83 1326
Biso mean--39.19 44.4 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071285
X-RAY DIFFRACTIONf_angle_d0.9681740
X-RAY DIFFRACTIONf_chiral_restr0.06203
X-RAY DIFFRACTIONf_plane_restr0.005221
X-RAY DIFFRACTIONf_dihedral_angle_d17.243807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0027-2.09390.26081270.18861179130694
2.0939-2.20430.27821360.18391202133896
2.2043-2.34240.22941320.18271198133096
2.3424-2.52320.23771360.1911214135096
2.5232-2.77710.26671330.20951227136097
2.7771-3.17880.22861380.21031254139298
3.1788-4.00450.21841430.15821274141799
4.0045-42.90830.19611500.151356150699
Refinement TLS params.Method: refined / Origin x: 20.9158 Å / Origin y: 20.663 Å / Origin z: -10.5033 Å
111213212223313233
T0.1646 Å20.0241 Å20.018 Å2-0.2153 Å2-0.0115 Å2--0.1818 Å2
L3.4399 °20.8759 °2-0.993 °2-3.2336 °2-1.0348 °2--2.9747 °2
S0.0487 Å °0.1695 Å °0.177 Å °-0.0899 Å °0.0575 Å °-0.0598 Å °-0.0952 Å °-0.0308 Å °-0.091 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 180
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 82

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