+Open data
-Basic information
Entry | Database: PDB / ID: 6o4x | ||||||
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Title | Binary complex of native hAChE with 9-aminoacridine | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE | ||||||
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: 2.3 Å | ||||||
Authors | Gerlits, O. / Kovalevsky, A. / Radic, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem.Biol.Interact. / Year: 2019 Title: A new crystal form of human acetylcholinesterase for exploratory room-temperature crystallography studies. Authors: Gerlits, O. / Ho, K.Y. / Cheng, X. / Blumenthal, D. / Taylor, P. / Kovalevsky, A. / Radic, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o4x.cif.gz | 232.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o4x.ent.gz | 185 KB | Display | PDB format |
PDBx/mmJSON format | 6o4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o4x_validation.pdf.gz | 469.2 KB | Display | wwPDB validaton report |
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Full document | 6o4x_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 6o4x_validation.xml.gz | 43 KB | Display | |
Data in CIF | 6o4x_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/6o4x ftp://data.pdbj.org/pub/pdb/validation_reports/o4/6o4x | HTTPS FTP |
-Related structure data
Related structure data | 6o4wC 6o50C 6o52C 4ey4S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 60287.977 Da / Num. of mol.: 2 / Fragment: residues 32-578 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-NO3 / | #4: Chemical | #5: 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 grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 10 mM sodium citrate, 100 mM HEPES, pH 7, and 6-8 % PEG6000 or PEG3350 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 73282 / % possible obs: 78 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.546 / Num. unique obs: 8342 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY4 Resolution: 2.3→31.459 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→31.459 Å
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Refine LS restraints |
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LS refinement shell |
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