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- PDB-5ygv: Crystal structure of the abscisic acid receptor PYR1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 5ygv
TitleCrystal structure of the abscisic acid receptor PYR1 in complex with an antagonist
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR
Function / homology
Function and homology information


positive regulation of response to water deprivation / : / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity ...positive regulation of response to water deprivation / : / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyketide cyclase / dehydrase and lipid transport / 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-8V6 / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAkiyama, T. / Sue, M. / Takeuchi, J. / Mimura, N. / Okamoto, M. / Monda, K. / Iba, K. / Ohnishi, T. / Todoroki, Y. / Yajima, S.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structure-Based Chemical Design of Abscisic Acid Antagonists That Block PYL-PP2C Receptor Interactions.
Authors: Takeuchi, J. / Mimura, N. / Okamoto, M. / Yajima, S. / Sue, M. / Akiyama, T. / Monda, K. / Iba, K. / Ohnishi, T. / Todoroki, Y.
History
DepositionSep 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 PYR1
B: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6544
Polymers50,8652
Non-polymers7892
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-12 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.203, 38.203, 263.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Abscisic acid receptor PYR1 / ABI1-binding protein 6 / Protein PYRABACTIN RESISTANCE 1 / Regulatory components of ABA receptor 11


Mass: 25432.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O49686
#2: Chemical ChemComp-8V6 / (2Z,4E)-3-methyl-5-[(1S,4S)-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid


Mass: 394.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.89 Å3/Da / Density % sol: 34.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 16% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12089 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 20.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.536 / Num. unique obs: 638 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WG8

3wg8


Resolution: 2.5→35 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.331 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.219 / ESU R Free: 0.363 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29395 647 5.1 %RANDOM
Rwork0.25579 ---
obs0.25758 12089 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.939 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.21 Å2
Refinement stepCycle: 1 / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 58 18 2819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022854
X-RAY DIFFRACTIONr_bond_other_d0.0030.022664
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9683865
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0056156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06923.233133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71715503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.271528
X-RAY DIFFRACTIONr_chiral_restr0.0640.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213087
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02591
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7014.5681355
X-RAY DIFFRACTIONr_mcbond_other1.7024.5671354
X-RAY DIFFRACTIONr_mcangle_it3.0436.8271685
X-RAY DIFFRACTIONr_mcangle_other3.0436.8281686
X-RAY DIFFRACTIONr_scbond_it1.4124.831499
X-RAY DIFFRACTIONr_scbond_other1.4124.8321500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.487.1472181
X-RAY DIFFRACTIONr_long_range_B_refined5.03752.7033046
X-RAY DIFFRACTIONr_long_range_B_other5.03652.7043047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.504→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 61 -
Rwork0.326 834 -
obs--91.23 %

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