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Yorodumi- PDB-7rb7: Room temperature structure of hAChE in complex with substrate ana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rb7 | ||||||
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Title | Room temperature structure of hAChE in complex with substrate analog 4K-TMA and MMB4 oxime | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / acetylcholine esterase / serine hydrolase / tetrahedral intermediate / oxime reactivator | ||||||
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 / acetylcholinesterase / amyloid precursor protein metabolic process / 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 / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / Synthesis, secretion, and deacylation of Ghrelin / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / collagen binding / synapse assembly / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / nervous system development / amyloid-beta binding / cell adhesion / hydrolase activity / 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: 2.6 Å | ||||||
Authors | Kovalevsky, A. / Gerlits, O. / Radic, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2021 Title: Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure Authors: Gerlits, O. / Blakeley, M.P. / Keen, D.A. / Radic, Z. / Kovalevsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rb7.cif.gz | 223.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rb7.ent.gz | 178.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rb7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7rb7_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7rb7_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 7rb7_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/7rb7 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/7rb7 | HTTPS FTP |
-Related structure data
Related structure data | 7rb5C 7rb6C 6o5rS 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 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 | #3: Chemical | #4: 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: 4.93 Å3/Da / Density % sol: 75.08 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 10 mM sodium citrate, 6-8% PEG6000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.997 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 69461 / % possible obs: 97.8 % / Redundancy: 2.7 % / CC1/2: 0.95 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7031 / CC1/2: 0.404 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6O5R Resolution: 2.6→39.185 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 23.76 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.185 Å
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Refine LS restraints |
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LS refinement shell |
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