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- PDB-7snu: Crystal structure of ShHTL7 from Striga hermonthica in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7snu
TitleCrystal structure of ShHTL7 from Striga hermonthica in complex with strigolactone antagonist RG6
ComponentsHyposensitive to light 7
KeywordsHYDROLASE / Parasite / Strigolactone / Receptor / Antagonist
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / metal ion binding / ACETATE ION / Chem-HFJ / IMIDAZOLE / Hyposensitive to light 7
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsArellano-Saab, A. / Stogios, P.J. / Skarina, T. / Yim, V. / Savchenko, A. / McCourt, P.
Funding support6items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)06752
Natural Sciences and Engineering Research Council (NSERC, Canada)507992
Natural Sciences and Engineering Research Council (NSERC, Canada)00356
Other governmentNFRFE-2018-00118
Natural Sciences and Engineering Research Council (NSERC, Canada)04298
Consejo Nacional de Ciencia y Tecnologia (CONACYT)
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A novel strigolactone receptor antagonist provides insights into the structural inhibition, conditioning, and germination of the crop parasite Striga.
Authors: Arellano-Saab, A. / McErlean, C.S.P. / Lumba, S. / Savchenko, A. / Stogios, P.J. / McCourt, P.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Hyposensitive to light 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,23911
Polymers30,2561
Non-polymers98310
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.216, 96.216, 69.358
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hyposensitive to light 7


Mass: 30255.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3PNA2

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Non-polymers , 6 types, 484 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-HFJ / 2-{(2S)-1-[(4-ethoxyphenyl)methyl]-4-[(2E)-3-(4-methoxyphenyl)prop-2-en-1-yl]piperazin-2-yl}ethan-1-ol / RG6


Mass: 410.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N2O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 M sodium acetate, 0.1 M imidazole pH 7.0, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97913 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 11, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. obs: 62389 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.94 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Net I/σ(I): 28.67
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2550 / CC1/2: 0.841 / Rpim(I) all: 0.233 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
HKL-30001.11data reduction
HKL-30001.11data scaling
PHENIX1.19.1_4122phasing
PHENIX1.19.1_4122model building
Coot0.9.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CBK

5cbk


Resolution: 1.46→28.68 Å / SU ML: 0.1155 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.2135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1615 1930 3.26 %
Rwork0.1275 57305 -
obs0.1286 59235 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.09 Å2
Refinement stepCycle: LAST / Resolution: 1.46→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 68 474 2640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642277
X-RAY DIFFRACTIONf_angle_d1.01223100
X-RAY DIFFRACTIONf_chiral_restr0.0943348
X-RAY DIFFRACTIONf_plane_restr0.0077397
X-RAY DIFFRACTIONf_dihedral_angle_d5.9206327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.2318880.1632568X-RAY DIFFRACTION59.01
1.5-1.540.17681100.14883246X-RAY DIFFRACTION74.51
1.54-1.580.19831340.13733918X-RAY DIFFRACTION89.31
1.58-1.630.17061350.12774038X-RAY DIFFRACTION93.5
1.63-1.690.16271420.12514235X-RAY DIFFRACTION96.45
1.69-1.760.16811400.13014273X-RAY DIFFRACTION97.98
1.76-1.840.13761470.12124323X-RAY DIFFRACTION99.11
1.84-1.940.1581500.1274334X-RAY DIFFRACTION99.45
1.94-2.060.16651450.11924381X-RAY DIFFRACTION99.93
2.06-2.220.15791430.12394359X-RAY DIFFRACTION99.82
2.22-2.440.15231440.12474385X-RAY DIFFRACTION99.67
2.44-2.790.18681470.13694373X-RAY DIFFRACTION99.85
2.79-3.520.14511490.12984398X-RAY DIFFRACTION99.76
3.52-28.680.15741560.12234474X-RAY DIFFRACTION99.94

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