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Yorodumi- PDB-2jez: Mus musculus acetylcholinesterase in complex with tabun and HLo-7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jez | ||||||
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Title | Mus musculus acetylcholinesterase in complex with tabun and HLo-7 | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / ACETYLCHOLINESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / MUS MUSCULUS / GLYCOPROTEIN / SERINE ESTERASE / OXIME / MOUSE / HLO-7 / TABUN / SYNAPSE / MEMBRANE | ||||||
Function / homology | Function and homology information acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ekstrom, F. / Astot, C. / Pang, Y.P. | ||||||
Citation | Journal: Clin.Pharmacol.Ther. / Year: 2007 Title: Novel Nerve-Agent Antidote Design Based on Crystallographic and Mass Spectrometric Analyses of Tabun-Conjugated Acetylcholinesterase in Complex with Antidotes. Authors: Ekstrom, F.J. / Astot, C. / Pang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jez.cif.gz | 223 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jez.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jez_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2jez_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2jez_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 2jez_validation.cif.gz | 63.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/2jez ftp://data.pdbj.org/pub/pdb/validation_reports/je/2jez | HTTPS FTP |
-Related structure data
Related structure data | 2jeyC 2jf0C 1j06S 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: 60369.086 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) References: UniProt: P21836, acetylcholinesterase, carboxylesterase #2: Chemical | #3: Chemical | ChemComp-P6G / | #4: 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: 3.8 Å3/Da / Density % sol: 70 % |
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Crystal grow | pH: 7 / Details: 27-30 % PEG750MME, 0.1 M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.08191 |
Detector | Type: MARRESERACH / Detector: CCD / Date: Oct 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08191 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.14 Å / Num. obs: 57837 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J06 Resolution: 2.6→29.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.622 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TABUN REACTION PRODUCT COVALENTELY ATTACHED TO SER203.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.14 Å
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