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Yorodumi- PDB-6g1u: Crystal structure of Torpedo Californica acetylcholinesterase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g1u | ||||||||||||
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Title | Crystal structure of Torpedo Californica acetylcholinesterase in complex with 9-Amino-6-chloro-1,2,3,4-tetrahydro-10-methylacridin-10-ium | ||||||||||||
Components | Acetylcholinesterase | ||||||||||||
Keywords | HYDROLASE / Torpedo Californica acetylcholinesterase / AD / alzheimer disease | ||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||||||||
Authors | Coquelle, N. / Colletier, J.P. | ||||||||||||
Citation | Journal: Molecules / Year: 2018 Title: Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis. Authors: Galdeano, C. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Bartolini, M. / Perez, B. / Clos, M.V. / Silman, I. / Jean, L. / Colletier, J.P. / Renard, P.Y. / Munoz-Torrero, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g1u.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g1u.ent.gz | 204.9 KB | Display | PDB format |
PDBx/mmJSON format | 6g1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g1u ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1u | HTTPS FTP |
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-Related structure data
Related structure data | 6g1vC 6g1wC 2xi4S 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 / Sugars , 2 types, 9 molecules AB
#1: Protein | Mass: 63763.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 1068 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-E1K / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 200/50 mM MES pH 6.0 / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→45.715 Å / Num. obs: 138453 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XI4 Resolution: 1.79→45.72 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→45.72 Å
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Refine LS restraints |
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LS refinement shell |
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