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Yorodumi- PDB-8p22: X-ray structure of acetylcholine-binding protein (AChBP) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p22 | ||||||
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Title | X-ray structure of acetylcholine-binding protein (AChBP) in complex with IOTA376. | ||||||
Components | Acetylcholine-binding protein | ||||||
Keywords | CHOLINE-BINDING PROTEIN / Fragment based drug design / Acetylcholine-binding protein / choline-binding proteins | ||||||
Function / homology | Function and homology information acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic cleft / response to nicotine / neuron projection / synapse / membrane Similarity search - Function | ||||||
Biological species | Lymnaea stagnalis (great pond snail) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cederfelt, D. / Boronat, P. / Dobritzsch, D. / Hennig, S. / Fitzgerald, E.A. / de Esch, I.J.P. / Danielson, U.H. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Elucidating the regulation of ligand gated ion channels via biophysical studies of ligand-induced conformational dynamics of acetylcholine binding proteins Authors: Fitzgerald, E.A. / Cederfelt, D. / Boronat, P. / Aarmo Lund, B. / Dobritzsch, D. / de Esch, I.J.P. / Danielson, U.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p22.cif.gz | 420.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p22.ent.gz | 344.7 KB | Display | PDB format |
PDBx/mmJSON format | 8p22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/8p22 ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p22 | HTTPS FTP |
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-Related structure data
Related structure data | 8p11C 8p1eC 8p1fC 8q1tC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23454.029 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P58154 #2: Chemical | ChemComp-WNO / Mass: 254.330 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H18N4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 3350 3% Ammonium sulphate 1.8M HEPES buffer 0.1M, pH 7.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→999 Å / Num. obs: 101962 / % possible obs: 88.32 % / Redundancy: 2 % / CC1/2: 0.907 / Rrim(I) all: 0.1852 / Net I/σ(I): 7.41 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 10549 / CC1/2: 0.588 / Rrim(I) all: 0.8643 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.51 Å / Cor.coef. Fo:Fc: 0.945 / SU B: 11.666 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.376 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.067 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→49.51 Å
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Refine LS restraints |
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