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Yorodumi- PDB-5bw2: X-ray crystal structure of Aplysia californica acetylcholine bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bw2 | ||||||
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Title | X-ray crystal structure of Aplysia californica acetylcholine binding protein (Ac-AChBP) Y55W in complex with 2-Pyridin-3-yl-1-aza-bicyclo[2.2.2]octane; 2-(3-pyridyl)quinuclidine; 2-PQ (TI-4699) | ||||||
Components | Soluble acetylcholine receptor | ||||||
Keywords | ACETYLCHOLINE BINDING PROTEIN / AChBP / nicotine / acetylcholine | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aplysia californica (California sea hare) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Bobango, J. / Sankaran, B. / Park, J.F. / Wu, J. / Talley, T.T. | ||||||
Citation | Journal: To Be Published Title: Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs Authors: Bobango, J. / Sankaran, B. / Park, J.F. / 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 | 5bw2.cif.gz | 221.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bw2.ent.gz | 176.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/5bw2 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/5bw2 | HTTPS FTP |
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-Related structure data
Related structure data | 5bp0C 5brxC 2bynS 2byrS 2bysS 2pgzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26235.141 Da / Num. of mol.: 5 / Fragment: UNP residues 18-236 / Mutation: Y55W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Cell line (production host): HEK GNT1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8 #2: Chemical | ChemComp-4VU / ( #3: 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: 2.39 Å3/Da / Density % sol: 48.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.7% PEG 400, 0.085 M HEPES - Na pH 7.5, 1.7 M Ammonium Sulfate, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 88 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→61.98 Å / Num. obs: 57146 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.27→2.33 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ENSEMBLE OF 2BYN, 2BYR, 2BYS, AND 2PGZ Resolution: 2.27→61.98 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.53 / 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 mean: 35.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→61.98 Å
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Refine LS restraints |
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LS refinement shell |
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