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- PDB-9qk5: X-ray crystal structure of SlPYL1-Caffeic Acid complex -

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Basic information

Entry
Database: PDB / ID: 9qk5
TitleX-ray crystal structure of SlPYL1-Caffeic Acid complex
ComponentsSlPYL1-NIO
KeywordsPLANT PROTEIN / ABA receptor / SlPYL1 / Caffeic 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
CAFFEIC ACID / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)26,0934
Polymers25,7381
Non-polymers3543
Water2,342130
1
A: SlPYL1-NIO
hetero molecules

A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1868
Polymers51,4772
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3970 Å2
ΔGint-31 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.066, 90.066, 51.402
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-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4 / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
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: 1.45→33.87 Å / Num. obs: 41294 / % possible obs: 96.37 % / Redundancy: 1.34 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.79 / Net I/σ(I): 2.02
Reflection shellResolution: 1.45→1.502 Å / Num. unique obs: 14919 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→33.87 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 2040 4.94 %
Rwork0.1955 39252 -
obs0.1963 41292 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.42 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 22 130 1671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511584
X-RAY DIFFRACTIONf_angle_d0.83822157
X-RAY DIFFRACTIONf_chiral_restr0.0802250
X-RAY DIFFRACTIONf_plane_restr0.0072278
X-RAY DIFFRACTIONf_dihedral_angle_d12.6986569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.34061640.29362346X-RAY DIFFRACTION88.44
1.48-1.520.28761130.26912530X-RAY DIFFRACTION93.43
1.52-1.560.32911270.25172587X-RAY DIFFRACTION96.41
1.56-1.610.25081520.24352604X-RAY DIFFRACTION97.28
1.61-1.660.25361210.22612631X-RAY DIFFRACTION97.48
1.66-1.720.26661310.2342620X-RAY DIFFRACTION97.11
1.72-1.790.21981420.20432604X-RAY DIFFRACTION96.42
1.79-1.870.21451080.19922625X-RAY DIFFRACTION96.67
1.87-1.970.19461400.1862612X-RAY DIFFRACTION96.56
1.97-2.090.20481100.17582622X-RAY DIFFRACTION96.71
2.09-2.250.16871460.17812657X-RAY DIFFRACTION97.09
2.25-2.480.19551580.19412632X-RAY DIFFRACTION97.79
2.48-2.840.24421640.20942674X-RAY DIFFRACTION98.3
2.84-3.570.20221260.19222743X-RAY DIFFRACTION98.9
3.58-33.870.21380.17992765X-RAY DIFFRACTION96.9
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)
10.2051909753910.04834780977960.1974769815630.153171843171-0.3278916183870.770009735395-0.6565897594660.00624808691142-0.2718777245970.49956987019-0.01340434637970.5650948119470.0335630394881-0.405635718369-0.2028070652630.266646503515-0.06506822468460.1024827485120.228304343141-0.09999032953760.44764429055326.880845232423.633199629415.6308034697
20.115176405379-0.0968370213801-0.1545022508380.453467338771-0.08158146563270.248280236094-0.1769670383380.05895235809570.3029727614830.2573730203570.1398727896050.0270806519898-0.5503035738760.2178784952760.002734800356060.312772001763-0.02792647335020.01905281015560.206290916895-0.05731969351640.23207327893336.073880535425.610203303910.8667022379
30.3611101651480.522349905754-0.1955089638230.8949522498520.1909751076540.6785550326940.0928797150562-0.114959179830.3923480734640.105034490579-0.09520414107860.223954971763-0.0386286798829-0.1008228000440.001391975633310.1807236479050.00541896086390.0398024066660.217632595089-0.0229671527570.26762060466723.80169053219.537472099910.5350408562
40.1087278267430.04527504331320.05521507520450.218453788784-0.01592769737170.0799812249975-0.115326465435-0.09109596809650.232959226393-0.06533669773280.0332375320063-0.06219294979680.00271279694228-0.005431093635729.14990545751E-50.1810965346410.03754259559060.02423819364720.2243008232030.03222242514620.16751864064340.019493061213.7248995364-1.74014557124
50.480844537284-0.19745794558-0.07785743331560.195162281915-0.05835987308870.01441280660570.1248966972260.0585023114755-0.131939950667-0.209506582797-0.08863755520120.05846155431130.07339748190480.2334572235970.0002554871025440.235882576060.0311796582878-0.02031948898790.231508341184-0.001639945705020.17268024631527.24868682755.79508407894-4.37743631012
61.58234057764-0.2846645595830.05133079308790.3636444180970.3100068697120.400716402465-0.1110133205950.9769990097660.371756578887-1.087174839910.361606234165-0.194347814649-0.08811411061910.194125071050.2130118665650.4604639343740.00221342893053-0.01597015976970.4011566792480.08780370475570.2261750144723.7905028514.2841332086-15.5895538298
70.249869477182-0.4070518215920.1867957570330.757330882246-0.3585530940370.4005356741890.0613067486531-0.15252647296-0.453670424185-0.1860557468790.5722148726181.481031990540.297654989112-0.5194107372260.1801506160310.272793169428-0.0183725401024-0.07104334790490.2933969705290.1223811108310.48968701833116.38485776772.50918269325-2.98484700426
80.302541728874-0.211449097093-0.06133091907050.270121878427-0.250463802430.197962954230.1077897145470.01648657400390.399422342777-0.120131616015-0.1046794515080.314930622652-0.1158610067030.0419595225472-0.0005066441090950.2009297020230.00349253032093-0.005277089752020.1922697033920.04078497205630.21092934922524.916119224318.4086402884-4.15674407042
90.421712641572-0.0642200156714-0.1522895892770.0847073926730.007115217359880.119709220888-0.3063248366890.576492178377-0.8872675496950.2750717796020.0953339030910.5309186587670.852070072381-0.436372931119-0.02550805449620.339862537948-0.05225809378580.05826825861630.270870161164-0.03411204136060.43805470631313.198740385110.16407342974.16966830568
100.44467192513-0.3750166658340.4477127624710.949980450074-0.6885235996461.41696383978-0.01811488748050.0605744473382-0.1067913276220.0661256082588-0.04103849340070.0644788942986-0.08303415483390.0641137590312-0.007093347584590.149138800292-0.01693146950310.00746291358780.172096309454-0.01783644383650.17772606638831.162718160816.74471470017.84006520565
110.71658102230.5454708957480.4422072036591.91815963404-0.6987059206590.912569116813-0.0459751771829-0.0398247450569-0.196529544270.08209373010970.0070006092379-0.0124422270630.1978321252690.003653277159330.0001626252109320.2028157843781.44126066612E-5-0.004138322197750.1657738833150.02380531235710.1732822430731.38648899967.137151385827.08687195767
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 75 )58 - 7531 - 48
44chain 'A' and (resid 76 through 86 )76 - 8649 - 59
55chain 'A' and (resid 87 through 103 )87 - 10360 - 76
66chain 'A' and (resid 104 through 114 )104 - 11477 - 87
77chain 'A' and (resid 115 through 128 )115 - 12888 - 101
88chain 'A' and (resid 129 through 149 )129 - 149102 - 122
99chain 'A' and (resid 150 through 157 )150 - 157123 - 130
1010chain 'A' and (resid 158 through 189 )158 - 189131 - 162
1111chain 'A' and (resid 190 through 220 )190 - 220163 - 193

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