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Yorodumi- PDB-2y2u: Nonaged form of Mouse Acetylcholinesterase inhibited by VX-Update -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y2u | |||||||||
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Title | Nonaged form of Mouse Acetylcholinesterase inhibited by VX-Update | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / CHOLINESTERASE / METHYLPHOSPHONATE | |||||||||
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: 2.6 Å | |||||||||
Authors | Akfur, C. / Artursson, E. / Ekstrom, F. | |||||||||
Citation | Journal: To be Published Title: Methylphosphonate Adducts of Acetylcholinesterase Investigated by Time Correlated Single Photon Counting and X-Ray Crystallography Authors: Akfur, C. / Artursson, E. / Ekstrom, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y2u.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y2u.ent.gz | 182.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y2u_validation.pdf.gz | 809.2 KB | Display | wwPDB validaton report |
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Full document | 2y2u_full_validation.pdf.gz | 828.9 KB | Display | |
Data in XML | 2y2u_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 2y2u_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y2u ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y2u | HTTPS FTP |
-Related structure data
Related structure data | 2y2vC 1j06S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60340.047 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 Source method: isolated from a genetically manipulated source Details: CATALYTIC SER203 PHOSPHONYLATED BY VX / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase #2: Sugar | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-P33 / | #5: Water | ChemComp-HOH / | Nonpolymer details | RESIDUE SVX REPRESENTS | |
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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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE |
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Crystal grow | pH: 7.9 / Details: 26-30% (V/V) PEG 750MME, 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 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.03 Å / Num. obs: 61880 / % possible obs: 99.9 % / Observed criterion σ(I): 3.7 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J06 Resolution: 2.6→28.762 Å / SU ML: 0.73 / σ(F): 1.33 / Phase error: 22.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.076 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→28.762 Å
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Refine LS restraints |
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LS refinement shell |
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