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- PDB-3wg8: Crystal structure of the abscisic acid receptor PYR1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 3wg8
TitleCrystal structure of the abscisic acid receptor PYR1 in complex with an antagonist AS6
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR / Abscisic acid
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-6AS / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAkiyama, T. / Sue, M. / Takeuchi, J. / Okamoto, M. / Muto, T. / Endo, A. / Nambara, E. / Hirai, N. / Ohnishi, T. / Cutler, S.R. ...Akiyama, T. / Sue, M. / Takeuchi, J. / Okamoto, M. / Muto, T. / Endo, A. / Nambara, E. / Hirai, N. / Ohnishi, T. / Cutler, S.R. / Todoroki, Y. / Yajima, S.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Designed abscisic acid analogs as antagonists of PYL-PP2C receptor interactions
Authors: Takeuchi, J. / Okamoto, M. / Akiyama, T. / Muto, T. / Yajima, S. / Sue, M. / Seo, M. / Kanno, Y. / Kamo, T. / Endo, A. / Nambara, E. / Hirai, N. / Ohnishi, T. / Cutler, S.R. / Todoroki, Y.
History
DepositionJul 31, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8132
Polymers25,4321
Non-polymers3811
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Abscisic acid receptor PYR1
hetero molecules

A: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6264
Polymers50,8652
Non-polymers7612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.932, 66.932, 78.237
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-323-

HOH

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1 / Production host: Escherichia coli (E. coli) / References: UniProt: O49686
#2: Chemical ChemComp-6AS / (2Z,4E)-5-[(1S)-3-(hexylsulfanyl)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid


Mass: 380.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 0.1M HEPES, 1mM AS6, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 9381 / Num. obs: 9259 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K90

3k90


Resolution: 2.3→32.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28139 445 4.8 %RANDOM
Rwork0.2375 ---
obs0.2395 8811 98.87 %-
all-8912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.54 Å20 Å2
2--0.54 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 26 33 1467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191460
X-RAY DIFFRACTIONr_bond_other_d0.0030.021394
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9631977
X-RAY DIFFRACTIONr_angle_other_deg3.6033.0053203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2165173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0223.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37215257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1371514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211612
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02334
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 42 -
Rwork0.311 634 -
obs--99.12 %

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