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Yorodumi- PDB-2whq: Crystal structure of acetylcholinesterase, phosphonylated by sari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2whq | ||||||
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Title | Crystal structure of acetylcholinesterase, phosphonylated by sarin (aged) in complex with HI-6 | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / HI-6 / SYNAPSE / MEMBRANE / SECRETED / NEUROTRANSMITTER DEGRADATION / CHOLINESTERASE / SERINE ESTERASE / ALTERNATIVE SPLICING / CELL JUNCTION / CELL MEMBRANE / DISULFIDE BOND / AGED SARIN / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN | ||||||
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 / nuclear envelope / presynaptic membrane / 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: 2.15 Å | ||||||
Authors | Ekstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.G. / Schneider, G. / Pang, Y.P. | ||||||
Citation | Journal: Plos One / Year: 2009 Title: Structure of Hi-6Sarin-Acetylcholinesterase Determined by X-Ray Crystallography and Molecular Dynamics Simulation: Reactivator Mechanism and Design. Authors: Ekstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.G. / Schneider, G. / Pang, Y.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2whq.cif.gz | 453.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2whq.ent.gz | 373.9 KB | Display | PDB format |
PDBx/mmJSON format | 2whq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2whq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2whq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2whq_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 2whq_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2whq ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whq | HTTPS FTP |
-Related structure data
Related structure data | 2whpC 2whrC 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
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 60311.992 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 Source method: isolated from a genetically manipulated source Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN. THE COMPLEX WAS SUBSEQUENTLY AGED Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase #2: Sugar | |
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-Non-polymers , 5 types, 658 molecules
#3: Chemical | #4: Chemical | ChemComp-P6G / | #5: Chemical | ChemComp-PGE / #6: Chemical | ChemComp-PEG / | #7: 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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 26-30 % (V/V) 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: I911-3 / Wavelength: 1.041 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.041 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.2 Å / Num. obs: 110895 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 45.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.15→2.3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J06 Resolution: 2.15→29.089 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 20.38 / Stereochemistry target values: ML / Details: RESIDUES 258-264 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.001 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→29.089 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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