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Yorodumi- PDB-2ha2: Crystal structure of mouse acetylcholinesterase complexed with su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ha2 | |||||||||
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Title | Crystal structure of mouse acetylcholinesterase complexed with succinylcholine | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / HYDROLASE FOLD / SERINE ESTERASE / ACETYLCHOLINESTERASE / HOMODIMER / GLYCOSYLATED PROTEIN | |||||||||
Function / homology | Function and homology information acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / nuclear envelope / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / 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 / FOURIER SYNTHESIS / Resolution: 2.05 Å | |||||||||
Authors | Bourne, Y. / Radic, Z. / Sulzenbacher, G. / Kim, E. / Taylor, P. / Marchot, P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Substrate and product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding Authors: Bourne, Y. / Radic, Z. / Sulzenbacher, G. / Kim, E. / Taylor, P. / Marchot, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ha2.cif.gz | 242.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ha2.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ha2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ha2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2ha2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2ha2_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 2ha2_validation.cif.gz | 72.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/2ha2 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/2ha2 | HTTPS FTP |
-Related structure data
Related structure data | 2h9yC 2ha0C 2ha3C 2ha4C 2ha5C 2ha6C 2ha7C 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 59764.488 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / Variant (production host): LAMBDA ZAP / References: UniProt: P21836, acetylcholinesterase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-FUC / |
#4: Sugar |
-Non-polymers , 4 types, 769 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-P6G / | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | SCK(901) AND SCU(902) ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. SCK(951) AND SCU(952) ARE IN ...SCK(901) AND SCU(902) ARE IN ALTERNATE CONFORMATI |
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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: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 25-32% PEG550 MME or PEG600, 60-100mM HEPES or Na acetate, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 112415 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 1.4 / % possible all: 55.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1J06 Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.462 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.138 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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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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