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Yorodumi- PDB-5bwb: ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bwb | ||||||
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Title | ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA IN COMPLEX WITH THE BIS-IMIDAZOLIUM OXIME 2BIM-7 | ||||||
Components | Acetylcholinesterase | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / Acetylcholinesterase / Hydrolase-Hydrolase inhibitor complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Legler, P.M. / Millard, C.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime. Authors: Legler, P.M. / Soojhawon, I. / Millard, C.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bwb.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bwb.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/5bwb ftp://data.pdbj.org/pub/pdb/validation_reports/bw/5bwb | HTTPS FTP |
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-Related structure data
Related structure data | 5bwcC 2aceS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 1 / Fragment: UNP residues 22-558 / 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 | ChemComp-MES / | #4: Chemical | ChemComp-4VV / ( | #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: 4.11 Å3/Da / Density % sol: 70.07 % / Description: wedge shaped |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: Drop solution contained 36% PEG 200, 0.2 M MES buffer pH 5.7, 20 mM 2BIM-7. Reservoir solution contained 35% PEG 200. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Dec 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→56.15 Å / Num. obs: 32414 / % possible obs: 100 % / Redundancy: 13.58 % / Rsym value: 0.1245 / Net I/σ(I): 17.18 |
Reflection shell | Resolution: 2.57→2.66 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.4065 / Mean I/σ(I) obs: 5.59 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ACE Resolution: 2.57→56.15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.25 / 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: 33.291 Å2
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Refinement step | Cycle: 1 / Resolution: 2.57→56.15 Å
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Refine LS restraints |
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