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- PDB-7z1r: X-ray crystal structure of SLPYL1-E151D mutant ABA complex -

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Basic information

Entry
Database: PDB / ID: 7z1r
TitleX-ray crystal structure of SLPYL1-E151D mutant ABA complex
ComponentsSlPYL1-E151D ABA
KeywordsPLANT PROTEIN / SLPYL1 / ABA receptor protein
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / plasma membrane / 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 PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsInfantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119805RB-I00 Spain
CitationJournal: Front Plant Sci / Year: 2022
Title: Structure-Based Modulation of the Ligand Sensitivity of a Tomato Dimeric Abscisic Acid Receptor Through a Glu to Asp Mutation in the Latch Loop.
Authors: Infantes, L. / Rivera-Moreno, M. / Daniel-Mozo, M. / Benavente, J.L. / Ocana-Cuesta, J. / Coego, A. / Lozano-Juste, J. / Rodriguez, P.L. / Albert, A.
History
DepositionFeb 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D000: SlPYL1-E151D ABA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1734
Polymers25,7241
Non-polymers4493
Water1,802100
1
D000: SlPYL1-E151D ABA
hetero molecules

D000: SlPYL1-E151D ABA
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 52.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)52,3468
Polymers51,4492
Non-polymers8976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2880 Å2
ΔGint-12 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.808, 87.808, 55.184
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-E151D ABA


Mass: 25724.418 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-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.: 1 / Source method: obtained synthetically / Formula: C15H20O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate 1.6M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979182 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979182 Å / Relative weight: 1
ReflectionResolution: 1.601→44.66 Å / Num. obs: 32621 / % possible obs: 99.83 % / Redundancy: 15.5 % / Biso Wilson estimate: 28.09 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05089 / Rpim(I) all: 0.01344 / Rrim(I) all: 0.05267 / Net I/σ(I): 25.46
Reflection shellResolution: 1.601→1.658 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.8972 / Mean I/σ(I) obs: 2.95 / Num. unique obs: 3216 / CC1/2: 0.958 / CC star: 0.989 / Rpim(I) all: 0.235 / Rrim(I) all: 0.9281 / % possible all: 99.57

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Processing

Software
NameVersionClassification
XDSVERSION Feb 5, 2021 BUILT=20210205data reduction
PHENIX1.20_4459refinement
XDSVERSION Feb 5, 2021 BUILT=20210205data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MOB

5mob


Resolution: 1.601→44.66 Å / SU ML: 0.2223 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1648 5.06 %
Rwork0.1942 30922 -
obs0.1953 32570 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.17 Å2
Refinement stepCycle: LAST / Resolution: 1.601→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 31 100 1649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651605
X-RAY DIFFRACTIONf_angle_d0.84422187
X-RAY DIFFRACTIONf_chiral_restr0.0614253
X-RAY DIFFRACTIONf_plane_restr0.0092287
X-RAY DIFFRACTIONf_dihedral_angle_d6.5117235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.650.411450.32022520X-RAY DIFFRACTION99.59
1.65-1.70.31221360.31282538X-RAY DIFFRACTION99.59
1.7-1.760.32921310.30622554X-RAY DIFFRACTION99.67
1.76-1.830.30081520.23752533X-RAY DIFFRACTION99.74
1.83-1.920.21451390.21822568X-RAY DIFFRACTION99.89
1.92-2.020.25161140.19622544X-RAY DIFFRACTION99.81
2.02-2.140.24481450.22532578X-RAY DIFFRACTION99.78
2.14-2.310.19671150.1942600X-RAY DIFFRACTION99.93
2.31-2.540.24471590.21232557X-RAY DIFFRACTION99.93
2.54-2.910.29171430.21852584X-RAY DIFFRACTION99.93
2.91-3.660.21271360.19012622X-RAY DIFFRACTION99.96
3.66-44.660.15831330.15952724X-RAY DIFFRACTION99.86
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)
10.02040522881440.0970301176946-0.004891460152350.1063658800210.02430250452290.0761809748278-0.164330176853-0.1703466442980.0140963790739-0.0258117326858-0.023349607750.1229385589620.0182423427412-0.3170099475928.67378517252E-50.4066410586650.04660982410860.108986620050.3565825997930.01791490514870.365281453225-7.2144590390234.76542904448.39031592212
20.786032662819-0.4325793169280.08876379706690.958228150047-0.01568156415850.5725557817820.0312187579036-0.09087589240890.1462742392550.07319267581930.059901769760.024323348181-0.0616614402425-0.04467973115534.45714513071E-50.3081117457550.00191066315190.02944587004850.2997327710790.001293124667330.244933543032-2.150119946436.872375244-0.0170558531147
31.118291790990.09193105802690.05088456482720.522598559718-0.006972389393751.010131720280.03323453379950.135440974162-0.182270842234-0.1858915381790.05279149975870.0767176738035-0.02649441411290.07898264272552.9803130951E-50.33121708812-0.00768526892611-0.04035298262670.301813337499-0.0008004058396210.2849768436521.4884933908424.3190170999-13.9114740677
40.998419809435-0.5015701282320.2520778269180.3309790841960.1123940321590.6750039418020.0756206994109-0.0574110290325-0.1724571878430.06875670920430.002606608092650.0923541759105-0.0428518103751-0.07527830208967.73355871779E-60.275895854855-0.005178380241710.003335151951570.2759263060470.03101945661130.25704905887-2.2573198659829.5009139307-4.18395812592
50.487148699989-0.3010519412180.3216540872210.234192256244-0.02988888170030.36449717021-0.122455231398-0.178011482184-0.171759135541-0.09837707604170.0284944337742-0.1292903274890.02918083239930.0738982407382-0.0002095682996730.278092703002-0.001689290958780.0160635318560.2632126509050.03549792019160.29249260932-0.68034097438229.21104116051.8628051875
60.965296901946-0.750620725610.5508504853610.8599167949160.138365372150.5927014117760.0232942104269-0.3036845461170.2253507423980.0524783692827-0.0250651514514-0.163076997196-0.03201770259290.146474806183-0.0001771750035220.2892203649950.0118503044706-0.006532719942910.291826603642-0.02705739730980.2823446973118.295328081629.3290138464-0.526941001236
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: D000 / 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 86 )44 - 8617 - 59
33chain 'A' and (resid 87 through 141 )87 - 14160 - 114
44chain 'A' and (resid 142 through 170 )142 - 170115 - 143
55chain 'A' and (resid 171 through 189 )171 - 189144 - 162
66chain 'A' and (resid 190 through 220 )190 - 220163 - 193

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