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- PDB-9gnl: X-ray crystal structure of VvPYL1 with ABA -

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Basic information

Entry
Database: PDB / ID: 9gnl
TitleX-ray crystal structure of VvPYL1 with ABA
ComponentsAbscisic acid receptor PYR1
KeywordsPLANT PROTEIN / VvPYL1 / ABA receptor protein
Function / homology
Function and homology information


protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
Chem-A8S / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRivera-Moreno, M. / Benavente, J.L. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: Physiol.Plantarum / Year: 2024
Title: Chemical activation of ABA signaling in grapevine through the iSB09 and AMF4 ABA receptor agonists enhances water use efficiency.
Authors: Bono, M. / Ferrer-Gallego, R. / Pou, A. / Rivera-Moreno, M. / Benavente, J.L. / Mayordomo, C. / Deis, L. / Carbonell-Bejerano, P. / Pizzio, G.A. / Navarro-Paya, D. / Matus, J.T. / Martinez- ...Authors: Bono, M. / Ferrer-Gallego, R. / Pou, A. / Rivera-Moreno, M. / Benavente, J.L. / Mayordomo, C. / Deis, L. / Carbonell-Bejerano, P. / Pizzio, G.A. / Navarro-Paya, D. / Matus, J.T. / Martinez-Zapater, J.M. / Albert, A. / Intrigliolo, D.S. / Rodriguez, P.L.
History
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)48,6204
Polymers48,0912
Non-polymers5292
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-16 kcal/mol
Surface area17840 Å2
Unit cell
Length a, b, c (Å)57.535, 49.621, 65.950
Angle α, β, γ (deg.)90.000, 99.725, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 34 through 219 or resid 301))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISGLNGLNAA34 - 21925 - 211
d_12A8SA8SA8SA8SAC301
d_21HISHISGLNGLNBB34 - 21925 - 211
d_22A8SA8SA8SA8SBD301

NCS oper: (Code: givenMatrix: (-0.930106578665, 0.351876790046, 0.105282842621), (0.365418849894, 0.857641183721, 0.361829606483), (0.0370245387021, 0.37501243261, -0.926280119036)Vector: -5. ...NCS oper: (Code: given
Matrix: (-0.930106578665, 0.351876790046, 0.105282842621), (0.365418849894, 0.857641183721, 0.361829606483), (0.0370245387021, 0.37501243261, -0.926280119036)
Vector: -5.86919638375, -5.54745136265, 32.8508999443)

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Components

#1: Protein Abscisic acid receptor PYR1


Mass: 24045.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: VIT_02s0012g01270
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F6HT94
#2: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid


Mass: 264.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.86 Å3/Da / Density % sol: 33.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, pH 5.0, 0.2 M magnesium chloride, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.4→46.83 Å / Num. obs: 47169 / % possible obs: 98.25 % / Redundancy: 3.3 % / Biso Wilson estimate: 57.76 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.102 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.489 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 14366 / CC1/2: 0.62 / Rpim(I) all: 0.922 / % possible all: 96.83

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.83 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.9738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3058 --
Rwork0.2333 13548 -
obs-14259 98.26 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 38 10 3047
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.25004845257 Å
Refinement TLS params.Method: refined / Origin x: -1.80614616923 Å / Origin y: 3.56783535208 Å / Origin z: 17.3710055238 Å
111213212223313233
T0.409970778148 Å2-0.0309442011758 Å20.00934995616573 Å2-0.43027428291 Å2-0.033111026634 Å2--0.361676552118 Å2
L3.80928293599 °2-0.299151874154 °2-0.417226058228 °2-1.19522122316 °20.0207268502727 °2--1.66743637179 °2
S-0.0218468120666 Å °-0.34087975212 Å °0.324433292951 Å °0.105478913788 Å °-0.0265219730206 Å °0.118351642756 Å °-0.109869637924 Å °-0.0990898966538 Å °0.000164620800681 Å °
Refinement TLS groupSelection details: all

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