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Yorodumi- PDB-3wtl: Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wtl | ||||||
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Title | Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Nitromethylene Analogue of Imidacloprid | ||||||
Components | Acetylcholine-binding protein | ||||||
Keywords | SIGNALING PROTEIN / neonicotinoids / nicotinic acetylcholine receptor / imidacloprid / 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: 2.3 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 | 3wtl.cif.gz | 226.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wtl.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wtl_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3wtl_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3wtl_validation.xml.gz | 46 KB | Display | |
Data in CIF | 3wtl_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/3wtl ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wtl | HTTPS FTP |
-Related structure data
Related structure data | 3wthC 3wtiC 3wtjC 3wtkC 3wtmC 3wtnC 3wtoC 2zjuS S: Starting model for refinement 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: 24221.811 Da / Num. of mol.: 5 / 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-N1Y / #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: 2.34 Å3/Da / Density % sol: 47.36 % |
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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 Nitromethylene Analogue of Imidacloprid, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.919 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2007 |
Radiation | Monochromator: fixed-exit double crystal (Si(111)) monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.59 Å / Num. all: 50742 / Num. obs: 48577 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.2 / Num. unique all: 5092 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZJU Resolution: 2.3→47.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2811565.02 / 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: 56.9228 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→47.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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