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Yorodumi- PDB-3wtn: Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wtn | ||||||
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Title | Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid | ||||||
Components | Acetylcholine-binding protein | ||||||
Keywords | SIGNALING PROTEIN / neonicotinoids / nicotinic acetylcholine receptor / imidacloprid / acetylcholine binding | ||||||
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: 2.09 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 | 3wtn.cif.gz | 454 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wtn.ent.gz | 373.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/3wtn ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wtn | HTTPS FTP |
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-Related structure data
Related structure data | 3wthC 3wtiC 3wtjC 3wtkC 3wtlC 3wtmC 3wtoC 2zjuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 24221.811 Da / Num. of mol.: 10 / Fragment: UNP residues 21-229 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-N2Y / ( #3: Chemical | ChemComp-CD / #4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 13, 2008 |
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: 2.09→50 Å / Num. all: 137631 / Num. obs: 131277 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.8 / Num. unique all: 12230 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZJU Resolution: 2.09→47.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2790612.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.3895 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.09→47.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.22 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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