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Yorodumi- PDB-7snu: Crystal structure of ShHTL7 from Striga hermonthica in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7snu | |||||||||||||||||||||
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Title | Crystal structure of ShHTL7 from Striga hermonthica in complex with strigolactone antagonist RG6 | |||||||||||||||||||||
Components | Hyposensitive to light 7 | |||||||||||||||||||||
Keywords | HYDROLASE / Parasite / Strigolactone / Receptor / Antagonist | |||||||||||||||||||||
Function / homology | Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / ACETATE ION / Chem-HFJ / IMIDAZOLE / Hyposensitive to light 7 Function and homology information | |||||||||||||||||||||
Biological species | Striga hermonthica (purple witchweed) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | |||||||||||||||||||||
Authors | Arellano-Saab, A. / Stogios, P.J. / Skarina, T. / Yim, V. / Savchenko, A. / McCourt, P. | |||||||||||||||||||||
Funding support | 6items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7snu.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7snu.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 7snu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/7snu ftp://data.pdbj.org/pub/pdb/validation_reports/sn/7snu | HTTPS FTP |
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-Related structure data
Related structure data | 5cbkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-IMD / | #6: Chemical | ChemComp-HFJ / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 M sodium acetate, 0.1 M imidazole pH 7.0, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97913 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 11, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→28.68 Å
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Refine LS restraints |
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LS refinement shell |
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