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Yorodumi- PDB-3wti: Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wti | ||||||
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Title | Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Clothianidin | ||||||
Components | Acetylcholine-binding protein | ||||||
Keywords | SIGNALING PROTEIN / neonicotinoids / nicotinic acetylcholine receptor / clothianidin / acetylcholine binding | ||||||
Function / homology | Function and homology information acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / postsynapse / neuron projection / membrane Similarity search - Function | ||||||
Biological species | Lymnaea stagnalis (great pond snail) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Okajima, T. / Ihara, M. / Yamashita, A. / Oda, T. / Matsuda, K. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2014 Title: Studies on an acetylcholine binding protein identify a basic residue in loop G on the beta 1 strand as a new structural determinant of neonicotinoid actions Authors: Ihara, M. / Okajima, T. / Yamashita, A. / Oda, T. / Asano, T. / Matsui, M. / Sattelle, D.B. / Matsuda, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wti.cif.gz | 423.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wti.ent.gz | 364.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/3wti ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wti | HTTPS FTP |
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-Related structure data
Related structure data | 3wthC 3wtjC 3wtkC 3wtlC 3wtmC 3wtnC 3wtoC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24250.875 Da / Num. of mol.: 5 / Fragment: UNP residues 21-229 / Mutation: Q55R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pPICZ B / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P58154 #2: Chemical | ChemComp-CT4 / #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N- ...AUTHORS STATE THAT BEFORE CRYSTALLIZ | |
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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: 2.3 Å3/Da / Density % sol: 46.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.7 Details: 0.2M Na citrate pH 5.7, 15-22% PEG3350, 0.5mM clothianidin, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 15, 2007 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→39.6 Å / Num. all: 30602 / Num. obs: 30565 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.67→2.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→39.6 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.864 / SU B: 44.925 / SU ML: 0.412 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.398 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.68→39.6 Å
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Refine LS restraints |
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