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Yorodumi- PDB-1n5r: Crystal structure of the mouse acetylcholinesterase-propidium complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n5r | |||||||||
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Title | Crystal structure of the mouse acetylcholinesterase-propidium complex | |||||||||
Components | acetylcholinesterase | |||||||||
Keywords | HYDROLASE / SERINE ESTERASE / ACETYLCHOLINESTERASE / HOMODIMER / HYDROLASE FOLD / GLYCOSYLATED PROTEIN | |||||||||
Function / homology | Function and homology information acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis ...acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / laminin binding / side of membrane / synapse assembly / collagen binding / neuromuscular junction / response to insulin / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / hydrolase activity / cell adhesion / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å | |||||||||
Authors | Bourne, Y. / Taylor, P. / Radic, Z. / Marchot, P. | |||||||||
Citation | Journal: EMBO J. / Year: 2003 Title: Structural insights into ligand interactions at the acetylcholinesterase peripheral anionic site Authors: Bourne, Y. / Taylor, P. / Radic, Z. / Marchot, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n5r.cif.gz | 222.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n5r.ent.gz | 181.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n5r ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n5r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59764.488 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) Variant (production host): LAMBDA-ZAP, LAMBDA-FIX CDNA, GENOMIC DNA References: UniProt: P21836, acetylcholinesterase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar |
-Non-polymers , 5 types, 425 molecules
#4: Chemical | ChemComp-P6G / | ||||
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#5: Chemical | ChemComp-PRM / | ||||
#6: Chemical | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.37 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 600, SODIUM ACETATE, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / PH range low: 8 / PH range high: 6.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.79 Å / Num. obs: 95908 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.041 / Net I/σ(I): 13.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 549001 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→39.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2288092.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.8561 Å2 / ksol: 0.331952 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→39.79 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 2 % / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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