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- PDB-7z1p: X-ray crystal structure of SLPYL1-E151D mutant -

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Basic information

Entry
Database: PDB / ID: 7z1p
TitleX-ray crystal structure of SLPYL1-E151D mutant
ComponentsSLPYL1-E151D
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
Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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
A: SLPYL1-E151D


Theoretical massNumber of molelcules
Total (without water)25,7241
Polymers25,7241
Non-polymers00
Water1,29772
1
A: SLPYL1-E151D

A: SLPYL1-E151D


Theoretical massNumber of molelcules
Total (without water)51,4492
Polymers51,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.969, 89.969, 51.768
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


Mass: 25724.418 Da / Num. of mol.: 1 / Mutation: E151D
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 47.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate 1.8M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979261 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979261 Å / Relative weight: 1
ReflectionResolution: 1.82→44.98 Å / Num. obs: 21962 / % possible obs: 99.76 % / Redundancy: 16.4 % / Biso Wilson estimate: 38.73 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05691 / Rpim(I) all: 0.01465 / Rrim(I) all: 0.05881 / Net I/σ(I): 23.84
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 16.3 % / Rmerge(I) obs: 1.979 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 2149 / CC1/2: 0.896 / Rpim(I) all: 0.4977 / Rrim(I) all: 2.042 / % possible all: 99.16

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Processing

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

5moa


Resolution: 1.82→44.98 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 1064 4.85 %
Rwork0.2094 20893 -
obs0.211 21957 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.06 Å2
Refinement stepCycle: LAST / Resolution: 1.82→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 72 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721552
X-RAY DIFFRACTIONf_angle_d0.97892115
X-RAY DIFFRACTIONf_chiral_restr0.0637250
X-RAY DIFFRACTIONf_plane_restr0.0106273
X-RAY DIFFRACTIONf_dihedral_angle_d5.3046211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.90.48411230.41062538X-RAY DIFFRACTION98.48
1.9-20.35151260.2882620X-RAY DIFFRACTION99.85
2-2.130.2911260.2562575X-RAY DIFFRACTION99.78
2.13-2.290.2451210.24862596X-RAY DIFFRACTION99.89
2.29-2.520.26991200.25132616X-RAY DIFFRACTION99.64
2.52-2.890.29531210.24982642X-RAY DIFFRACTION99.96
2.89-3.640.25721540.21592606X-RAY DIFFRACTION100
3.64-44.980.20221730.16352700X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 1.63014664679 Å / Origin y: 30.8149453295 Å / Origin z: -5.41587322678 Å
111213212223313233
T0.313368317976 Å2-0.0130397287979 Å2-0.00753404686905 Å2-0.344165274931 Å20.00826133946939 Å2--0.337117353158 Å2
L0.922671844513 °2-0.419884850228 °20.350254880519 °2-0.925057103091 °2-0.203138605218 °2--1.63986415715 °2
S0.00455620213387 Å °0.137051047672 Å °-0.203517117402 Å °0.0897403025823 Å °0.082784149221 Å °0.0953665419965 Å °0.0323136090489 Å °-0.0107782253217 Å °-3.84664070981E-6 Å °
Refinement TLS groupSelection details: all

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