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Yorodumi- PDB-6fld: Carbamylated T. californica acetylcholineterase bound to uncharge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fld | |||||||||
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Title | Carbamylated T. californica acetylcholineterase bound to uncharged hybrid reactivator 1 | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / Acetylcholinesterase Hybrid reactivators Organophosphate inhibition Structure-based optimization | |||||||||
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 / Resolution: 2.4 Å | |||||||||
Authors | De la Mora, E. / Santoni, G. / de Souza, J. / Sussman, J. / Silman, I. / Baati, R. / Weik, M. / Nachon, F. | |||||||||
Funding support | France, 2items
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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 | 6fld.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fld.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/6fld ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6fld | HTTPS FTP |
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-Related structure data
Related structure data | 6fqnC 6g17C 6g4mC 6g4nC 6g4oC 6g4pC 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, 4 molecules A
#1: Protein | Mass: 60279.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetronarce californica (Pacific electric ray) Gene: ache Production host: Tetronarce californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase |
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#2: Sugar |
-Non-polymers , 5 types, 222 molecules
#3: Chemical | ChemComp-DQ5 / | ||||
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#4: Chemical | ChemComp-1PG / | ||||
#5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.4 / Details: PEG 200 30 %, MES 100 mM pH 5.4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→37.32 Å / Num. obs: 40520 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 43.62 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Resolution: 2.4→37.32 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 24.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→37.32 Å
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Refine LS restraints |
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LS refinement shell |
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