+Open data
-Basic information
Entry | Database: PDB / ID: 7b2w | ||||||
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Title | Torpedo californica acetylcholinesterase complexed with UO2 | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / acetylcholinesterase / ASSAM / differential scanning calorimetry / divalent metal ion / electron paramagnetic resonance / thermal inactivation / Torpedo / 4D motif / 3.1.1.7 | ||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Tetronarce californica (Pacific electric ray) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Silman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L. | ||||||
Citation | Journal: Protein Sci. / Year: 2021 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: Journal: Bull Soc Ophtalmol Fr / Year: 1987 Title: [Treatment of vitreous hemorrhages. Rare causes]. Authors: Aracil, P. #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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b2w.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b2w.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 7b2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/7b2w ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b2w | HTTPS FTP |
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-Related structure data
Related structure data | 7b38C 7b8eC 1ea5S 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
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetronarce californica (Pacific electric ray) Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.74 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: The use of standard vapor diffusion techniques in hanging drop with 61 percent saturated ammonium sulfate, 360 nM Na,K-phosphate buffer pH 7.0, as the precipating agent and a protein ...Details: The use of standard vapor diffusion techniques in hanging drop with 61 percent saturated ammonium sulfate, 360 nM Na,K-phosphate buffer pH 7.0, as the precipating agent and a protein concentration of ~11 mg/ml together with UO2(NO3)2. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.541 Å |
Detector | Type: SIEMENS-XENTRONICS / Detector: AREA DETECTOR / Date: Jul 10, 1990 |
Radiation | Monochromator: Graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→39.0924 Å / Num. obs: 23867 / % possible obs: 84.24 % / Biso Wilson estimate: 36.6 Å2 / Rsym value: 0.115 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.65→2.77 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2116 / Rsym value: 0.09 / % possible all: 57.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EA5 Resolution: 2.65→39.09 Å / SU ML: 0.3211 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 20.046 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: 35.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→39.09 Å
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Refine LS restraints |
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LS refinement shell |
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