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Open data
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Basic information
Entry | Database: PDB / ID: 7b8e | ||||||
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Title | Torpedo californica acetylcholinesterase complexed with Ca+2 | ||||||
![]() | Acetylcholinesterase | ||||||
![]() | HYDROLASE / acetylcholinesterase / ASSAM / differential scanning calorimetry / divalent metal ion / electron paramagnetic resonance / thermal inactivation / Torpedo / 4D motif / 3.1.1.7 | ||||||
Function / homology | ![]() acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. | ||||||
![]() | ![]() Title: Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif. Authors: Silman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L. #1: ![]() Title: X-ray structures of Torpedo californica acetylcholinesterase complexed with (+)-huperzine A and (-)-huperzine B: structural evidence for an active site rearrangement. Authors: Dvir, H. / Jiang, H.L. / Wong, D.M. / Harel, M. / Chetrit, M. / He, X.C. / Jin, G.Y. / Yu, G.L. / Tang, X.C. / Silman, I. / Bai, D.L. / Sussman, J.L. #2: Journal: Science / Year: 1991 Title: Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein. Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.8 KB | Display | ![]() |
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PDB format | ![]() | 98.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b2wC ![]() 7b38C ![]() 1ea5S 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#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: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 254 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/FWN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FWN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Chemical | ChemComp-FWN / | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: By mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M calcium acetate/10-15% ...Details: By mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M calcium acetate/10-15% (v/v) polyethylene glycol (PEG) 5000 monomethyl ether, 0.1 M MES, pH 6.5), thus yielding crystals of the Ca+2/TcAChE complex. |
-Data collection
Diffraction | Mean temperature: 155 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→19.96 Å / Num. obs: 38704 / % possible obs: 99.36 % / Redundancy: 4 % / Biso Wilson estimate: 39.68 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 3752 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EA5 Resolution: 2.23→19.96 Å / SU ML: 0.2692 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1504 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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