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- PDB-6nwc: PYL10 bound to the ABA pan-agonist 3CB -

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Basic information

Entry
Database: PDB / ID: 6nwc
TitlePYL10 bound to the ABA pan-agonist 3CB
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-L6P / Abscisic acid receptor PYL10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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: Science / Year: 2019
Title: Dynamic control of plant water use using designed ABA receptor agonists.
Authors: Vaidya, A.S. / Helander, J.D.M. / Peterson, F.C. / Elzinga, D. / Dejonghe, W. / Kaundal, A. / Park, S.Y. / Xing, Z. / Mega, R. / Takeuchi, J. / Khanderahoo, B. / Bishay, S. / Volkman, B.F. / ...Authors: Vaidya, A.S. / Helander, J.D.M. / Peterson, F.C. / Elzinga, D. / Dejonghe, W. / Kaundal, A. / Park, S.Y. / Xing, Z. / Mega, R. / Takeuchi, J. / Khanderahoo, B. / Bishay, S. / Volkman, B.F. / Todoroki, Y. / Okamoto, M. / Cutler, S.R.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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)17,5732
Polymers17,2471
Non-polymers3261
Water43224
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)67.630, 67.630, 63.776
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 17246.676 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-L6P / 1-{[(4-cyano-3-cyclopropylphenyl)acetyl]amino}cyclohexane-1-carboxylic acid


Mass: 326.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7 / Details: 33% Tacsimate

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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: Nov 20, 2017 / Details: VariMax-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 7327 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 53.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.028 / Rrim(I) all: 0.096 / Net I/σ(I): 32
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 359 / CC1/2: 0.818 / Rpim(I) all: 0.348 / Rrim(I) all: 1.076 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.05 Å43.14 Å
Translation5.05 Å43.14 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.0phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NWB

6nwb


Resolution: 2.35→43.138 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.87
RfactorNum. reflection% reflection
Rfree0.2581 703 9.94 %
Rwork0.1979 --
obs0.2039 7073 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.88 Å2 / Biso mean: 56.1686 Å2 / Biso min: 34.98 Å2
Refinement stepCycle: final / Resolution: 2.35→43.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 24 24 1256
Biso mean--56.13 52.26 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061252
X-RAY DIFFRACTIONf_angle_d0.8251694
X-RAY DIFFRACTIONf_chiral_restr0.054200
X-RAY DIFFRACTIONf_plane_restr0.006214
X-RAY DIFFRACTIONf_dihedral_angle_d16.214781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.53140.31591290.25981159128890
2.5314-2.78620.33011400.25281235137595
2.7862-3.18920.30821380.2411280141898
3.1892-4.01760.27261510.189413041455100
4.0176-43.14550.21371450.174213921537100

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