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- PDB-9qk6: X-ray crystal structure of SlPYL1-FeruloylPhenylalanine complex -

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Basic information

Entry
Database: PDB / ID: 9qk6
TitleX-ray crystal structure of SlPYL1-FeruloylPhenylalanine complex
ComponentsSlPYL1-NIO
KeywordsPLANT PROTEIN / ABA receptor / SlPYL1 / Feruloyl Phenylalanine
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
: / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)26,1583
Polymers25,7381
Non-polymers4192
Water1,06359
1
A: SlPYL1-NIO
hetero molecules

A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3166
Polymers51,4772
Non-polymers8394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2530 Å2
ΔGint-5 kcal/mol
Surface area18180 Å2
Unit cell
Length a, b, c (Å)90.042, 90.042, 50.997
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-A1I70 / (2~{S})-2-[[(~{E})-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enoyl]amino]-3-phenyl-propanoic acid


Mass: 341.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19NO5 / 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.: 59 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
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: Oct 25, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→77.98 Å / Num. obs: 24319 / % possible obs: 99.88 % / Redundancy: 1.34 % / Biso Wilson estimate: 27.97 Å2 / CC1/2: 0.923 / Net I/σ(I): 3.46
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 2407 / CC1/2: 0.923

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→77.98 Å / SU ML: 0.2333 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 1251 5.14 %
Rwork0.2019 23068 -
obs0.2041 24319 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.81 Å2
Refinement stepCycle: LAST / Resolution: 1.75→77.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 29 59 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01351579
X-RAY DIFFRACTIONf_angle_d1.34832147
X-RAY DIFFRACTIONf_chiral_restr0.0882250
X-RAY DIFFRACTIONf_plane_restr0.0134285
X-RAY DIFFRACTIONf_dihedral_angle_d14.8397583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.33261270.31092543X-RAY DIFFRACTION99.78
1.82-1.90.28291350.23582529X-RAY DIFFRACTION99.85
1.9-20.24581590.20382513X-RAY DIFFRACTION99.96
2-2.130.24881450.20032541X-RAY DIFFRACTION99.93
2.13-2.290.28511490.20742537X-RAY DIFFRACTION99.85
2.29-2.520.21071080.21242579X-RAY DIFFRACTION99.81
2.52-2.890.23971460.23022554X-RAY DIFFRACTION99.96
2.89-3.640.26741240.21142601X-RAY DIFFRACTION99.96
3.64-77.980.22411580.17262671X-RAY DIFFRACTION99.89
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)
10.1454789445210.211119403384-0.06138200508460.335398432163-0.2929919708340.72180164686-0.6713809356040.08002943428980.7833777147090.3687247016060.217166526119-0.285138416191-0.0924955173592-0.1425282798-0.0004291122347090.399233248781-0.0614078888416-0.1413519849640.3466868281570.03743170328670.47077164652-7.23294503298-34.9932489501-15.0275497112
20.2963122640460.286370983975-0.03979433215480.227691692207-0.1116851131260.3607972321150.1743416342760.0745167559881-0.484056203353-0.0845396930639-0.118816375190.4590516938410.291453693882-0.4508698042260.0003784777488280.395060821348-0.0573693255451-0.08664751383540.330881542375-0.003501989571380.384685436216-4.2448018093-44.0847790078-10.346600036
30.14712887424-0.1814840444020.1959702366140.227969199519-0.1281035183710.244546795720.0164360508316-0.299184230599-0.166329073807-0.1988263693520.143539123340.2813182643090.00532293128798-0.140391121391-9.01605241973E-50.2981355719030.0361994632298-0.02430426684520.2753768997320.02585721367440.365415215878-4.94632460873-30.3571715977-10.2333359952
40.4524187062620.00622476569999-0.157526811750.38112178611-0.1397860031740.1000165291120.0144071048581-0.210484689879-0.122740044928-0.02413948477980.0289667106924-0.1540444609690.07572804410730.141740719536-2.39765205787E-50.2857286253550.02747299843150.004048747418830.3699710572360.004778239215160.2824193444628.46842841032-31.60021407653.8277198985
50.1518404428420.0088895774468-0.02228457911080.05972176986690.005911326721440.0238431322451-0.266757736819-0.7964729614430.4542245118180.2548573317710.1008652676770.461345602899-0.2015808996250.307127581082-0.004850208463050.3636520532480.08180630516650.09194698267550.586589479505-0.01573977327620.297666588535-0.692227352598-27.189794655715.4662730346
61.316788927-0.33533622674-0.5742613420630.07652868990180.1123023258040.1806282752670.4884455370190.2838316640871.175521482740.489939550865-0.0117551318644-0.267397787778-0.770215882654-0.2822513006480.03953150785050.3852454170470.01843779167390.06853718842350.4010817264360.01503785275490.443100055126.18546010093-15.37185269972.37638195637
70.470442542192-0.299239829780.4499845613020.149652841162-0.3082783008010.698189862359-0.0816590742667-0.254440263950.105724948050.2223477098750.2811740687860.6422040744370.0083119457646-0.0431651811475-0.0001014213571280.2843314858170.01085697574870.04109478315180.313214866080.03688006946220.309459951091-3.14351333704-29.9837181354.39181538256
80.02687221045870.04477264305980.06407860907810.02398882097660.07151613119980.1428595910890.1192990667570.2309309017350.928542507884-0.05402381057440.0527008494889-0.167379336444-1.109645051410.1731553632550.0006779018988380.49026261318-0.01821323334580.02244571987420.3514779377810.04054785925540.501212119423-2.5994833312-15.7431304132-3.82005337068
90.82054582907-0.0177807293603-0.620517480080.1676908173370.2579776523381.15157557318-0.178663360676-0.05426441363290.266880228720.1204554577610.150483935155-0.2820900058220.05594707284210.0203792932587-0.0005256149880470.280782980440.005962429990350.01644582356320.2285504872680.02363860017050.2772626952161.15817378131-35.3478295309-7.54821151107
101.146129565040.703481996466-0.6872566383040.938267236855-0.05050969216640.4930632977210.0932912789080.225801344644-0.116777388709-0.265457554837-0.0683635417230.06233958628160.1885987841550.216462402397-4.25458071047E-50.283099978067-0.01009043157230.02763573318170.284326291931-0.0238784503670.2310459377999.42790544641-30.7783203184-6.99042501824
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 103 )76 - 10349 - 76
55chain 'A' and (resid 104 through 114 )104 - 11477 - 87
66chain 'A' and (resid 115 through 127 )115 - 12788 - 100
77chain 'A' and (resid 128 through 149 )128 - 149101 - 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 220 )190 - 220163 - 193

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