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Yorodumi- PDB-7pdb: Crystal structure of Lymnaea stagnalis Acetylcholine-binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pdb | ||||||
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Title | Crystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP) Q55R/M114V double mutant complexed with Flupyradifurone | ||||||
Components | Acetylcholine-binding protein | ||||||
Keywords | SIGNALING PROTEIN / Acetylcholine / protein / insecticide | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmembrane signaling receptor activity / synapse / membrane Similarity search - Function | ||||||
Biological species | Lymnaea stagnalis (great pond snail) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Montgomery, M.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators. Authors: Montgomery, M. / Rendine, S. / Zimmer, C.T. / Elias, J. / Schaetzer, J. / Pitterna, T. / Benfatti, F. / Skaljac, M. / Bigot, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pdb.cif.gz | 208.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pdb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/7pdb ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pdb | HTTPS FTP |
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-Related structure data
Related structure data | 7pd6C 7pdrC 7pe5C 7pe6C 1uv6S S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 23818.428 Da / Num. of mol.: 5 / Mutation: Q55R, N66D, M114V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Komagataella pastoris (fungus) / References: UniProt: P58154 #2: Chemical | ChemComp-7IE / #3: Water | ChemComp-HOH / | 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: 2.29 Å3/Da / Density % sol: 46.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 14-18% PEG3350, 0.1-0.25M diammonium hydrogen citrate, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→31.12 Å / Num. obs: 45552 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 44.053 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.032 / Rrim(I) all: 0.095 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.33→2.52 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 9383 / Rpim(I) all: 0.207 / Rrim(I) all: 0.574 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UV6 Resolution: 2.33→31.119 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.232 / Average fsc free: 0.8719 / Average fsc work: 0.8829 / Cross valid method: FREE R-VALUE / ESU R: 0.459 / ESU R Free: 0.263 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.647 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→31.119 Å
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Refine LS restraints |
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