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- PDB-9qk4: X-ray crystal structure of SlPYL1-Ferulic Acid complex -

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Basic information

Entry
Database: PDB / ID: 9qk4
TitleX-ray crystal structure of SlPYL1-Ferulic Acid complex
ComponentsSlPYL1-NIO
KeywordsPLANT PROTEIN / ABA receptor / SlPYL1 / Ferulic Acid
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / : / START-like domain superfamily
Similarity search - Domain/homology
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRivera-Moreno, M. / Merino-Gracia, J. / Infantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: Plant Physiol Biochem. / Year: 2025
Title: Natural modulators of abscisic acid Signaling: Insights into polyphenol-based antagonists and their role in ABA receptor regulation.
Authors: Merino, J. / Rivera-Moreno, M. / Bono, M. / Nunez-Villanueva, D. / Gonzalez-Vega, A. / Mayordomo, C. / Infantes, L. / Chikhale, R. / Rodriguez, P.L. / Albert, A.
History
DepositionMar 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0113
Polymers25,7381
Non-polymers2722
Water54030
1
A: SlPYL1-NIO
hetero molecules

A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0226
Polymers51,4772
Non-polymers5454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)89.642, 89.642, 50.369
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein SlPYL1-NIO


Mass: 25738.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: 101268417 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q7HTY9
#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7 / Details: 3.5 M ammonium sulfate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→44.93 Å / Num. obs: 14889 / % possible obs: 92.62 % / Redundancy: 1.35 % / Biso Wilson estimate: 31.83 Å2 / CC1/2: 0.87 / Net I/σ(I): 2.86
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 761 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.82 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.0339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 713 4.79 %
Rwork0.2278 14176 -
obs0.2298 14889 92.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.15 Å2
Refinement stepCycle: LAST / Resolution: 2→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 18 30 1563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231563
X-RAY DIFFRACTIONf_angle_d0.49872126
X-RAY DIFFRACTIONf_chiral_restr0.0425249
X-RAY DIFFRACTIONf_plane_restr0.0035274
X-RAY DIFFRACTIONf_dihedral_angle_d13.7514565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.4791080.35542717X-RAY DIFFRACTION88.86
2.15-2.370.35181350.31432745X-RAY DIFFRACTION90.82
2.37-2.710.3451440.29822828X-RAY DIFFRACTION93.2
2.71-3.410.26191560.23873014X-RAY DIFFRACTION99.31
3.46-44.820.21941700.17452872X-RAY DIFFRACTION94.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2514313362250.310143509160.2023237402460.2403021642590.3340776185780.74326098032-0.2158073752640.183134328263-0.04963585847950.4941280834440.05308368377981.227358786590.149076492020.284950117103-0.0001312004538520.4921776735980.04755136266520.1532158049450.543864389474-0.08157124430181.0071569500333.673729671311.3470536642-6.46866159037
20.317203055831-0.2799511985690.06028509374770.125918929755-0.1117011294540.344221854704-0.193040570585-0.158782303329-0.274966206411-0.05855014348470.247927402289-1.186014423920.1103402510060.452876746972-9.16067241832E-60.5292301706890.0141294216435-0.02968692149790.646366215063-0.1234002217490.58084706318739.988956818318.2250912873-1.72773136216
31.33573310004-0.599596588439-0.7393823174470.5597633952161.0560280830.55196419164-0.02743550500170.1077781337960.02387585652980.1483179432110.0169204781336-0.01112531998170.113238964390.02175768148056.16230650588E-50.4869359561340.0158333215382-0.06093493147970.400217133358-0.01941393932610.63497651617429.755791860817.21587414693.00694993381
40.272040902584-0.1452143630260.3098587773450.6142904593580.3350479725370.155079118463-0.3198754073650.05002670718380.431040389926-0.04382775179150.04698107528890.27308803112-0.1888253148980.02992330243880.0001083552645440.4951157661780.019933395653-0.02470743714490.385228322748-0.1056780442490.53400018283919.976111359921.234526433312.7927134992
50.531913019120.48175871892-0.2401861056680.485740187258-0.2536303552770.1537420385760.334605404179-0.332843481427-0.6469515887240.405423943961-0.1413875620880.2802621310440.226145335282-0.276013165554-9.14228693599E-60.7115442874740.0198584970353-0.03083263218820.5858196776780.09231973308510.46185959618720.039733336614.857931118521.7490032781
60.899475156024-1.586056264950.9078503424933.65108236942-1.795704371030.6499187471320.548563957916-0.867113119004-0.919034285734-0.08789925867530.3597755433511.917525345670.691638175503-0.6396808030160.2164282881450.641098955824-0.02148636234730.03126736752450.5704699546410.05922688517730.60693183515910.29286912513.252775408811.2246018566
70.352611801299-0.404325582351-0.01177790668791.149548488540.7425780974850.8427761637150.130324686295-0.3927170298-0.20258096340.3608011140710.08930929705-0.2089476467040.00658821501613-0.0626335109009-4.75131276282E-50.504308763818-0.000456584394824-0.05953901803320.4429516111650.02450161765750.50361588737626.76683001312.176824245113.0015867297
80.0627869634419-0.164244374648-0.2088858609640.1955911555530.3395052987040.4215510724860.3426358540150.704703091881-1.23423068121-0.318214297384-0.5017481716161.497300589860.0886195951521-0.317462813901-0.0007251283265010.5455212535630.0117687843036-0.06859539785010.5201720210960.02787004149580.85753067718914.78570613186.504720528464.81665750755
90.817607816438-0.4559959706850.7437207374940.953582310019-0.2365381995310.7225554110220.1064020443490.1030015078150.07106984118530.239441140519-0.04105271028710.2585408444050.02230254489220.03445559517799.08648661128E-60.461367540698-0.0208232819255-0.05035877682210.473484556694-0.002553513563610.44551112274629.866306112118.60186297361.00751316778
101.632470065540.1485188064720.5956157803270.04530385729210.632771188067-0.4051885402320.1026992701970.1289335260610.00390701648264-0.255876038228-0.0422199666281-0.39399292137-0.161678711961-0.115983973946-0.0001016143131040.55606140219-0.00207794082873-0.01171532400430.4953529177330.04762535142920.37492521617321.536993140823.40138168491.40285082529
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 43 )28 - 431 - 16
22chain 'A' and (resid 44 through 57 )44 - 5717 - 30
33chain 'A' and (resid 58 through 86 )58 - 8631 - 59
44chain 'A' and (resid 87 through 98 )87 - 9860 - 71
55chain 'A' and (resid 99 through 114 )99 - 11472 - 87
66chain 'A' and (resid 115 through 126 )115 - 12688 - 99
77chain 'A' and (resid 127 through 149 )127 - 149100 - 122
88chain 'A' and (resid 150 through 157 )150 - 157123 - 130
99chain 'A' and (resid 158 through 189 )158 - 189131 - 162
1010chain 'A' and (resid 190 through 219 )190 - 219163 - 192

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