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- PDB-5ydh: Crystal structure of acetylcholinesterase catalytic subunits of t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ydh | ||||||||||||
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Title | Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, 3.2 A | ||||||||||||
![]() | Acetylcholinesterase | ||||||||||||
![]() | HYDROLASE / ALPHA/BETA HYDROLASE | ||||||||||||
Function / homology | ![]() acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Han, Q. / Guan, H. / Robinson, H. / Ding, H. / Liao, C. / Li, J. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Crystal structures of acetylcholinesterase of the malaria vector Anopheles gambiae reveal a polymerization interface, ligand binding residues and post translational modifications Authors: Han, Q. / Guan, H. / Ding, H. / Liao, C. / Robinson, H. / Li, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231 KB | Display | ![]() |
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PDB format | ![]() | 185.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 54.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ydiC ![]() 5ydjC ![]() 4nqh S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 64393.395 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 162-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Ace, ACE1, ACHE1, AGAP001356 / Plasmid: PPICZ*A / Production host: ![]() |
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-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-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: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar |
-Non-polymers , 5 types, 46 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.84 Å3/Da / Density % sol: 78.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES BUFFER, 1.6M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2013 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.21→56.51 Å / Num. obs: 43806 / % possible obs: 63 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.21→3.38 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NQH ![]() 4nqh Resolution: 3.21→55.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.015 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.697 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 84.29 Å2
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Refinement step | Cycle: LAST / Resolution: 3.21→55.93 Å
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Refine LS restraints |
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