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- PDB-2xud: Crystal structure of the Y337A mutant of mouse acetylcholinesterase -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xud | ||||||
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Title | Crystal structure of the Y337A mutant of mouse acetylcholinesterase | ||||||
![]() | ACETYLCHOLINESTERASE | ||||||
![]() | HYDROLASE / HYDROLASE FOLD | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bourne, Y. / Radic, Z. / Taylor, P. / Marchot, P. | ||||||
![]() | ![]() Title: Conformational Remodeling of Femtomolar Inhibitor-Acetylcholinesterase Complexes in the Crystalline State Authors: Bourne, Y. / Radic, Z. / Taylor, P. / Marchot, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 423.1 KB | Display | ![]() |
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PDB format | ![]() | 349.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 55.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xufC ![]() 2xugC ![]() 2xuhC ![]() 2xuiC ![]() 2xujC ![]() 2xukC ![]() 2xuoC ![]() 2xupC ![]() 2xuqC ![]() 1j06S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
NCS oper:
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Components
#1: Protein | Mass: 59672.395 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DECAMATHONIUM PARTIALLY BOUND IN CHAIN A / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DME / | #4: Chemical | ChemComp-P6G / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | ACETATE (ACT): FAVORABLE DISTANCE TO BE COVALENTLY LINKED TO CATALYTIC SERINE DI(HYDROXYETHYL)ETHER ...ACETATE (ACT): FAVORABLE DISTANCE TO BE COVALENTLY | Sequence details | EXPRESSED REGION 32-574 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM PEG-600 25-35% (V/V) IN 50-100 MM HEPES, PH 6.0-7.0, OR WITH PEG-550 MME 30% (V/V) IN 50 MM NA ACETATE, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. obs: 57806 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 57.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J06 Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.23 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.587 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→20 Å
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Refine LS restraints |
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