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- PDB-7z1q: X-ray crystal structure of SLPYL1-E151D mutant with NIO molecules -

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Basic information

Entry
Database: PDB / ID: 7z1q
TitleX-ray crystal structure of SLPYL1-E151D mutant with NIO molecules
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 / 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: 1.683 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2516
Polymers25,7241
Non-polymers5265
Water1,78399
1
A: SlPYL1-E151D
hetero molecules

A: SlPYL1-E151D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,50212
Polymers51,4492
Non-polymers1,05310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4710 Å2
ΔGint-27 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.160, 87.160, 55.276
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
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.: 2 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
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 / Ambient temp details: Synchrotron / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.683→44.6 Å / Num. obs: 27741 / % possible obs: 99.84 % / Redundancy: 9.8 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04322 / Rpim(I) all: 0.01428 / Rrim(I) all: 0.04557 / Net I/σ(I): 31.29
Reflection shellResolution: 1.683→1.744 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.9637 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 2726 / CC1/2: 0.79 / CC star: 0.939 / Rpim(I) all: 0.3954 / Rrim(I) all: 1.045

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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: 1.683→44.6 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2204 1431 5.16 %
Rwork0.1998 26296 -
obs0.2011 27727 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.89 Å2
Refinement stepCycle: LAST / Resolution: 1.683→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 35 99 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651585
X-RAY DIFFRACTIONf_angle_d0.87322156
X-RAY DIFFRACTIONf_chiral_restr0.0602249
X-RAY DIFFRACTIONf_plane_restr0.0085278
X-RAY DIFFRACTIONf_dihedral_angle_d6.3539218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.683-1.740.49591120.392612X-RAY DIFFRACTION99.05
1.74-1.810.37071200.30652617X-RAY DIFFRACTION100
1.81-1.90.26081650.22932595X-RAY DIFFRACTION100
1.9-20.24731330.19652588X-RAY DIFFRACTION99.82
2-2.120.21751270.22912634X-RAY DIFFRACTION100
2.12-2.280.25821490.2112620X-RAY DIFFRACTION99.86
2.28-2.510.23231300.21912646X-RAY DIFFRACTION99.93
2.51-2.880.26311650.22122604X-RAY DIFFRACTION100
2.88-3.630.22551590.19482647X-RAY DIFFRACTION99.96
3.63-44.60.17381710.16562733X-RAY DIFFRACTION99.79
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)
11.645937524430.1479360871470.1559817075363.058822700330.03806360168411.129221797740.0450038332263-0.08256077894040.1019179566140.01585811918580.02319226861280.2947635063-0.0289146926204-0.153726105748-0.0663730054490.2139139569540.0063875216729-0.01498931512210.2492412079640.03031489176930.205002297763-0.95972816038234.3595582243-1.15902712989
24.98944850101-2.148610935251.02311312223.300993364630.1309996828041.553327169870.4677739011690.359083623904-0.288207180947-1.03788038164-0.1793974028650.4448873654910.345263704933-0.0771849636676-0.2432707149030.432352255355-0.00414253737165-0.1095458632690.30024186063-0.02959461536910.268834602462.28407588419.4626844633-16.3033996758
32.370787439580.684445316265-0.2999793858412.825417788240.1368744717072.47302052852-0.0310580925526-0.00443513148767-0.154401552592-0.2120869243090.1417628794540.3397250383970.077866984752-0.101676753676-0.09962824207160.218967579393-0.000183438212277-0.07710101638670.2280277431730.01985849224270.282133468085-4.1980803042324.1188020121-9.17643249649
42.957656589111.2235743023-0.1950816962274.41290970951-1.217917120762.60422214845-0.0036291100523-0.189282021055-0.154198120453-0.03756200764570.076770413956-0.0217935622231-0.0707081056438-0.0253574031198-0.04041383194190.1866948386610.0216748755650.0006584198504670.2357775516220.01143119595410.1740338355190.17907539155934.2390038708-0.0599767947823
55.643616165041.78561340544-1.601303618387.25885828196-3.423722127985.341531701030.18083920452-0.4450482767610.06682206874770.224303072506-0.199379603684-0.300337038252-0.2072543832050.229730023420.05819145330160.2160108102890.0254975858638-0.03757486073710.209324319904-0.04619492627040.1940039588918.7160046941229.1586707384-0.844566644586
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 29 through 98 )29 - 981 - 70
22chain 'A' and (resid 99 through 126 )99 - 12671 - 98
33chain 'A' and (resid 127 through 157 )127 - 15799 - 129
44chain 'A' and (resid 158 through 189 )158 - 189130 - 161
55chain 'A' and (resid 190 through 219 )190 - 219162 - 191

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