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- PDB-3c84: Crystal structure of a complex of AChBP from aplysia californica ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c84 | ||||||
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Title | Crystal structure of a complex of AChBP from aplysia californica and the neonicotinoid thiacloprid | ||||||
![]() | Soluble acetylcholine receptor | ||||||
![]() | CHOLINE-BINDING PROTEIN / acetylcholine binding protein / neonicotinoid / Receptor | ||||||
Function / homology | ![]() acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Talley, T.T. / Harel, M. / Hibbs, R.E. / Tomizawa, M. / Casida, J.E. / Taylor, P.W. | ||||||
![]() | ![]() Title: Atomic interactions of neonicotinoid agonists with AChBP: molecular recognition of the distinctive electronegative pharmacophore. Authors: Talley, T.T. / Harel, M. / Hibbs, R.E. / Radic, Z. / Tomizawa, M. / Casida, J.E. / Taylor, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.7 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c79C ![]() 2bynS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25852.744 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line (production host): kidney HEK-293 / Production host: ![]() #2: Chemical | ChemComp-TH4 / {( #3: Chemical | ChemComp-IPA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% isopropanol, 0.2M magnesium chloride, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→87.4 Å / Num. all: 97540 / Num. obs: 94127 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9613 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BYN Resolution: 1.94→87.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.608 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / 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: 32.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→87.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.939→1.989 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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