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- PDB-7c8l: Hybrid designing of potent inhibitors of Striga strigolactone rec... -

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Basic information

Entry
Database: PDB / ID: 7c8l
TitleHybrid designing of potent inhibitors of Striga strigolactone receptor ShHTL7
ComponentsHyposensitive to light 7
KeywordsHYDROLASE / ShHTL7 / KK1007 / Covalent Inhibitor / Specificity / Striga
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / metal ion binding / pyrrolidine-1-carbaldehyde / Hyposensitive to light 7
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsShahul Hameed, U.F. / Arold, S.T.
CitationJournal: Plant Physiol. / Year: 2022
Title: Rational design of Striga hermonthica-specific seed germination inhibitors.
Authors: Zarban, R.A. / Hameed, U.F.S. / Jamil, M. / Ota, T. / Wang, J.Y. / Arold, S.T. / Asami, T. / Al-Babili, S.
History
DepositionJun 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)31,5966
Polymers30,6101
Non-polymers9865
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.474, 92.474, 80.256
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hyposensitive to light 7 / ShHTL7


Mass: 30610.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3PNA2

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Non-polymers , 5 types, 279 molecules

#2: Chemical ChemComp-EGC / 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL / TRITON X-100


Mass: 602.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FP6 / pyrrolidine-1-carbaldehyde


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 20% (w/v) PEG 8000, 100 mM MES/ Sodium hydroxide pH 6.0, 200 mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.449→46.24 Å / Num. obs: 68930 / % possible obs: 96.44 % / Redundancy: 18.7 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.93
Reflection shellResolution: 1.449→1.49 Å / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 5863 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z89

5z89


Resolution: 1.45→46.237 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 1903 2.85 %
Rwork0.1356 64772 -
obs0.1365 66675 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.95 Å2 / Biso mean: 28.5095 Å2 / Biso min: 16.57 Å2
Refinement stepCycle: final / Resolution: 1.45→46.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 54 274 2416
Biso mean--44.82 45.94 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.4850.29591210.2542402584
1.485-1.52520.29661160.2369421388
1.5252-1.57010.25491300.2075444592
1.5701-1.62080.22661330.1925445294
1.6208-1.67870.20771390.164462196
1.6787-1.74590.17611320.1459467998
1.7459-1.82540.18921400.1379471399
1.8254-1.92160.14341380.111476299
1.9216-2.0420.14011370.10914761100
2.042-2.19970.14121470.10744785100
2.1997-2.4210.16151390.12374788100
2.421-2.77130.15881470.12984810100
2.7713-3.49140.16881390.13134837100
3.4914-46.2370.16881450.14594881100

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