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Yorodumi- PDB-4zjt: X-ray crystal structure of Lymnaea stagnalis acetylcholine bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zjt | ||||||
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Title | X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB) | ||||||
Components | Acetylcholine-binding protein | ||||||
Keywords | ACETYLCHOLINE BINDING PROTEIN / nicotinic / AChBP / receptor / Anabaseine | ||||||
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: 1.85 Å | ||||||
Authors | Bobango, J. / Wu, J. / Talley, T.T. | ||||||
Citation | Journal: To Be Published Title: X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB) Authors: Bobango, J. / Wu, J. / Talley, T.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zjt.cif.gz | 434.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zjt.ent.gz | 353.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zjt ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zjt | HTTPS FTP |
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-Related structure data
Related structure data | 1uv6S 1uw6S 1ux2S 1yi5S 2zjuS 2zjvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24859.496 Da / Num. of mol.: 10 / Fragment: UNP residues 20-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P58154 #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-4P6 / ( #4: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.26 M ammonium phosphate, 35% glycerol |
-Data collection
Diffraction | Mean temperature: 88 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2011 |
Diffraction measurement | Details: 1.00 degrees, 1.0 sec, detector distance 250.00 mm |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.077 / Number: 1708039 |
Reflection | Resolution: 1.74→50 Å / Num. obs: 248133 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/av σ(I): 22.167 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.035 / Mean I/σ(I) obs: 1.237 / Rsym value: 0.688 / % possible all: 68.5 |
Cell measurement | Reflection used: 1708039 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1YI5, 1UV6, 1UW6, 1UX2, 2ZJU, 2ZJV Resolution: 1.85→49.985 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.68 Å2 / Biso mean: 26.4473 Å2 / Biso min: 12.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→49.985 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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