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Yorodumi- PDB-6g4n: Torpedo californica acetylcholinesterase bound to uncharged hybri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g4n | |||||||||
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Title | Torpedo californica acetylcholinesterase bound to uncharged hybrid reactivator 2 | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / acetylcholinesterase / tabun / nerve agent | |||||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Tetronarce californica (Pacific electric ray) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Santoni, G. / De la Mora, E. / de Souza, J. / Silman, I. / Sussman, J. / Baati, R. / Weik, M. / Nachon, F. | |||||||||
Funding support | France, 1items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents. Authors: Santoni, G. / de Sousa, J. / de la Mora, E. / Dias, J. / Jean, L. / Sussman, J.L. / Silman, I. / Renard, P.Y. / Brown, R.C.D. / Weik, M. / Baati, R. / Nachon, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g4n.cif.gz | 439.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g4n.ent.gz | 359 KB | Display | PDB format |
PDBx/mmJSON format | 6g4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g4n ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g4n | HTTPS FTP |
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-Related structure data
Related structure data | 6fldC 6fqnC 6g17C 6g4mC 6g4oC 6g4pC 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.: 2 / Source method: isolated from a natural source Source: (natural) Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 3.04 Å3/Da / Density % sol: 59.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 150 mM MES 36% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→46.3 Å / Num. obs: 33562 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rpim(I) all: 0.175 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.9→3 Å / CC1/2: 0.9 / Rpim(I) all: 0.883 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ea5 Resolution: 2.9→46.291 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.51 / 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: 2.9→46.291 Å
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Refine LS restraints |
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LS refinement shell |
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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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