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Yorodumi- PDB-5hf8: Crystal structure of human acetylcholinesterase in complex with p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hf8 | |||||||||
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Title | Crystal structure of human acetylcholinesterase in complex with paraoxon (alternative acyl loop conformation) | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / acetylcholinesterase | |||||||||
Function / homology | Function and homology information negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / 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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Franklin, M.F. / Rudolph, M.J. / Ginter, C. / Cassidy, M.S. / Cheung, J. | |||||||||
Citation | Journal: Proteins / Year: 2016 Title: Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface. Authors: Franklin, M.C. / Rudolph, M.J. / Ginter, C. / Cassidy, M.S. / Cheung, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hf8.cif.gz | 228.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hf8.ent.gz | 181.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hf8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5hf8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5hf8_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 5hf8_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/5hf8 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/5hf8 | HTTPS FTP |
-Related structure data
Related structure data | 5hf5C 5hf6C 5hf9C 5hfaC 4ey4S 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59447.105 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 33 to 574 / Mutation: none Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 5 types, 239 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-NO3 / | #8: 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: 4.38 Å3/Da / Density % sol: 71.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15 - 18% PEG3350, 0.2M potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→100 Å / Num. obs: 52628 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 53.54 Å2 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.037 / Rrim(I) all: 0.165 / Χ2: 1.087 / Net I/av σ(I): 24.421 / Net I/σ(I): 4.7 / Num. measured all: 1016991 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY4 Resolution: 2.8→49.916 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.34 / 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: 135.45 Å2 / Biso mean: 48.4735 Å2 / Biso min: 19.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→49.916 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: 18 / % reflection obs: 100 %
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