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- PDB-7z1s: X-ray crystal structure of SLPYL1-NIO complex -

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Basic information

Entry
Database: PDB / ID: 7z1s
TitleX-ray crystal structure of SLPYL1-NIO complex
ComponentsSlPYL1-NIO
KeywordsPLANT PROTEIN / SLPYL1 / 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
NICOTINIC ACID / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Assembly

Deposited unit
A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9543
Polymers25,7381
Non-polymers2152
Water1,38777
1
A: SlPYL1-NIO
hetero molecules

A: SlPYL1-NIO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9076
Polymers51,4772
Non-polymers4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3140 Å2
ΔGint-1 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.674, 86.674, 55.896
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-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
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: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.65→44.83 Å / Num. obs: 29543 / % possible obs: 99.6 % / Redundancy: 14 % / Biso Wilson estimate: 36.96 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04638 / Rpim(I) all: 0.01248 / Rrim(I) all: 0.04808 / Net I/σ(I): 27.19
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 13.8 % / Rmerge(I) obs: 3.333 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 2883 / CC1/2: 0.515 / CC star: 0.825 / Rpim(I) all: 0.9231 / Rrim(I) all: 3.461 / % possible all: 96.92

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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: 5MOA

5moa


Resolution: 1.65→44.83 Å / SU ML: 0.3481 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2697 1523 5.16 %
Rwork0.231 28020 -
obs0.2328 29543 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 15 77 1599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791659
X-RAY DIFFRACTIONf_angle_d0.96112260
X-RAY DIFFRACTIONf_chiral_restr0.0651263
X-RAY DIFFRACTIONf_plane_restr0.0084294
X-RAY DIFFRACTIONf_dihedral_angle_d6.5523230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.52991370.46942411X-RAY DIFFRACTION95.11
1.7-1.760.65321400.56592508X-RAY DIFFRACTION99.66
1.76-1.830.56291120.48532537X-RAY DIFFRACTION99.66
1.83-1.910.34721690.32522513X-RAY DIFFRACTION99.89
1.91-2.010.30411290.25372531X-RAY DIFFRACTION99.92
2.01-2.140.27971300.25532562X-RAY DIFFRACTION100
2.14-2.310.29541290.26422553X-RAY DIFFRACTION99.93
2.31-2.540.24921440.24922567X-RAY DIFFRACTION99.93
2.54-2.90.27891590.24752540X-RAY DIFFRACTION99.93
2.9-3.660.21361480.21812583X-RAY DIFFRACTION100
3.66-44.830.25331260.18212715X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.798669606701 Å / Origin y: -28.5860661118 Å / Origin z: -4.51856503006 Å
111213212223313233
T0.295054886134 Å2-0.0164423882567 Å20.0124555350218 Å2-0.271334746362 Å2-0.0307370977288 Å2--0.273480722806 Å2
L1.03024502597 °2-0.618484008048 °2-0.301828183654 °2-1.24366574416 °2-0.114495833886 °2--0.987803966312 °2
S0.0950587361208 Å °-0.047555393002 Å °0.0680553373811 Å °-0.0448240492503 Å °0.000860862034313 Å °-0.0820739810232 Å °-0.024052169 Å °0.0250858178576 Å °3.92531798321E-5 Å °
Refinement TLS groupSelection details: all

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