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Yorodumi- PDB-1f8u: CRYSTAL STRUCTURE OF MUTANT E202Q OF HUMAN ACETYLCHOLINESTERASE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f8u | |||||||||
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Title | CRYSTAL STRUCTURE OF MUTANT E202Q OF HUMAN ACETYLCHOLINESTERASE COMPLEXED WITH GREEN MAMBA VENOM PEPTIDE FASCICULIN-II | |||||||||
Components |
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Keywords | HYDROLASE/TOXIN / SERINE ESTERASE / HUMAN ACETYLCHOLINESTERASE / HYDROLASE / SNAKE TOXIN / HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-TOXIN COMPLEX | |||||||||
Function / homology | Function and homology information negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / amyloid precursor protein metabolic process / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / amyloid precursor protein metabolic process / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / laminin binding / side of membrane / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / amyloid-beta binding / nervous system development / positive regulation of cold-induced thermogenesis / toxin activity / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Dendroaspis angusticeps (eastern green mamba) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | |||||||||
Authors | Kryger, G. / Harel, M. / Shafferman, A. / Silman, I. / Sussman, J.L. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II. Authors: Kryger, G. / Harel, M. / Giles, K. / Toker, L. / Velan, B. / Lazar, A. / Kronman, C. / Barak, D. / Ariel, N. / Shafferman, A. / Silman, I. / Sussman, J.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f8u.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f8u.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 1f8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f8u ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f8u | HTTPS FTP |
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-Related 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: 64640.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY / References: UniProt: P22303, acetylcholinesterase |
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#2: Protein | Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Dendroaspis angusticeps (eastern green mamba) Secretion: VENOM / References: UniProt: P01403, UniProt: P0C1Z0*PLUS |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.61 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.009 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 50.3 Å2 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 25075 / % possible obs: 83.4 % / Num. measured all: 270951 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 20.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 2.9→39.43 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.89 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→39.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / Rfactor obs: 0.17 / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / Rfactor Rwork: 0.318 |