+Open data
-Basic information
Entry | Database: PDB / ID: 5e2i | ||||||
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Title | Acetylcholinesterase Methylene Blue no PEG | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | HYDROLASE / Inhibitor | ||||||
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 | Torpedo californica (Pacific electric ray) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Dym, O. | ||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex. Authors: Dym, O. / Song, W. / Felder, C. / Roth, E. / Shnyrov, V. / Ashani, Y. / Xu, Y. / Joosten, R.P. / Weiner, L. / Sussman, J.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 | 5e2i.cif.gz | 225.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e2i.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2i ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2i | HTTPS FTP |
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-Related structure data
Related structure data | 5dlpC 5e4jC 5e4tC 2w91S 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: 60193.977 Da / Num. of mol.: 1 / Fragment: UNP residues 25-556 / Source method: isolated from a natural source Source: (natural) Torpedo californica (Pacific electric ray) References: UniProt: P04058, acetylcholinesterase | ||||||
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#2: Sugar | #3: Chemical | #4: Chemical | ChemComp-DME / | #5: 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: 4.16 Å3/Da / Density % sol: 70.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG200 (v/v) in 100 mM NaCl/1 mM MES, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9394 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→45.9 Å / Num. obs: 29664 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.02 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2w91 Resolution: 2.65→45.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 17.117 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.345 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→45.62 Å
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Refine LS restraints |
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