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Yorodumi- PDB-2c58: Torpedo californica acetylcholinesterase in complex with 20mM ace... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c58 | ||||||
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Title | Torpedo californica acetylcholinesterase in complex with 20mM acetylthiocholine | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / SERINE ESTERASE / SYNAPSE / MEMBRANE / NEUROTRANSMITTER CLEAVAGE / ALPHA/BETA HYDROLASE / SUBSTRATE INHIBITION / ALTERNATIVE SPLICING / GLYCOPROTEIN / GPI-ANCHOR / LIPOPROTEIN / NEUROTRANSMITTER DEGRADATION | ||||||
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: 2.3 Å | ||||||
Authors | Colletier, J.P. / Fournier, D. / Greenblatt, H.M. / Sussman, J.L. / Zaccai, G. / Silman, I. / Weik, M. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structural Insights Into Substrate Traffic and Inhibition in Acetylcholinesterase. Authors: Colletier, J.P. / Fournier, D. / Greenblatt, H.M. / Stojan, J. / Sussman, J.L. / Zaccai, G. / Silman, I. / Weik, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c58.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c58.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 2c58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/2c58 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/2c58 | HTTPS FTP |
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-Related structure data
Related structure data | 2c4hC 2c5fC 2c5gC 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
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 60778.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray) Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase |
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#4: Sugar |
-Non-polymers , 5 types, 830 molecules
#2: Chemical | ChemComp-ETM / | ||||
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#3: Chemical | ChemComp-AT3 / | ||||
#5: Chemical | ChemComp-PGE / #6: Chemical | ChemComp-CL / #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: 3.8 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 277 K / pH: 6 Details: 32% PEG200, 150MM MES, PH6, 4DEG. C. THE CRYSTAL UNDERWENT 9 SUCCESSIVE SOAKINGS OF 1 HOUR PLUS 1 SOAKING OF 10 MINUTES IN 200 MICROLITER FRESH MOTHER LIQUOR SOLUTIONS, CONTAINING 20MM OF ...Details: 32% PEG200, 150MM MES, PH6, 4DEG. C. THE CRYSTAL UNDERWENT 9 SUCCESSIVE SOAKINGS OF 1 HOUR PLUS 1 SOAKING OF 10 MINUTES IN 200 MICROLITER FRESH MOTHER LIQUOR SOLUTIONS, CONTAINING 20MM OF THE SUBSTRATE ACETYLTHIOCHOLINE., pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 49453 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.14 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.63 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 7.31 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.43 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EA5 Resolution: 2.3→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3491345.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 98.5653 Å2 / ksol: 0.339188 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.34 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 20
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Xplor file |
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