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Yorodumi- PDB-2ace: NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ace | |||||||||
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Title | NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | SERINE HYDROLASE / NEUROTRANSMITTER CLEAVAGE / CATALYTIC TRIAD / ALPHA/BETA HYDROLASE | |||||||||
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: 2.5 Å | |||||||||
Authors | Harel, M. / Raves, M.L. / Silman, I. / Sussman, J.L. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A. Authors: Raves, M.L. / Harel, M. / Pang, Y.-P. / Silman, I. / Kozikowski, A.P. / Sussman, J.L. #1: Journal: Biochim.Biophys.Acta / Year: 1996 Title: Residues in Torpedo Californica Acetylcholinesterase Necessary for Processing to a Glycosyl Phosphatidylinositol-Anchored Form Authors: Bucht, G. / Hjalmarsson, K. #2: Journal: Protein Sci. / Year: 1994 Title: Structure and Dynamics of the Active Site Gorge of Acetylcholinesterase: Synergistic Use of Molecular Dynamics Simulation and X-Ray Crystallography Authors: Axelsen, P.H. / Harel, M. / Silman, I. / Sussman, J.L. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase Authors: Harel, M. / Schalk, I. / Ehret-Sabatier, L. / Bouet, F. / Goeldner, M. / Hirth, C. / Axelsen, P.H. / Silman, I. / Sussman, J.L. #4: Journal: Science / Year: 1991 Title: Atomic Structure of Acetylcholinesterase from Torpedo Californica: A Prototypic Acetylcholine-Binding Protein Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I. #5: Journal: J.Mol.Biol. / Year: 1988 Title: Purification and Crystallization of a Dimeric Form of Acetylcholinesterase from Torpedo Californica Subsequent to Solubilization with Phosphatidylinositol-Specific Phospholipase C Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Varon, L. / Toker, L. / Futerman, A.H. / Silman, I. #6: Journal: Nature / Year: 1986 Title: Primary Structure of Torpedo Californica Acetylcholinesterase Deduced from its Cdna Sequence Authors: Schumacher, M. / Camp, S. / Maulet, Y. / Newton, M. / Macphee-Quigley, K. / Taylor, S.S. / Friedmann, T. / Taylor, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ace.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ace.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ace.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/2ace ftp://data.pdbj.org/pub/pdb/validation_reports/ac/2ace | HTTPS FTP |
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-Related structure data
Related structure data | 1votC 1ace 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 on special symmetry positions |
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Details | TORPEDO CALIFONICA ACETYLCHOLINESTERASE IS A G2 DIMER IN SOLUTION (SEE SUSSMAN 1988). THE ASYMMETRIC UNIT CONTAINS A MONOMER, WITH THE CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING THE TWO MONOMERS IN A DIMER. |
-Components
#1: Protein | Mass: 60736.516 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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#2: Chemical | ChemComp-ACH / |
#3: Water | ChemComp-HOH / |
Compound details | THERE IS RECENT EVIDENCE (SEE BUCHT 1996) THAT THE GPI ANCHOR IS ATTACHED TO EITHER SER 543 OR SER ...THERE IS RECENT EVIDENCE (SEE BUCHT 1996) THAT THE GPI ANCHOR IS ATTACHED TO EITHER SER 543 OR SER 544, NOT TO CYS 537. |
-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: 5.8 Details: PROTEIN WAS CRYSTALLIZED FROM 35% PEG 200, 100 MM MES, PH 5.8, AT 4 DEG., temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25 Å / Num. obs: 46243 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.095 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.9 / Rsym value: 0.713 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 138332 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.621 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ACE 1ace Resolution: 2.5→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE NATURAL SUBSTRATE ACETYLCHOLINE, IN AN ALL-TRANS CONFORMATION, HAS BEEN MANUALLY DOCKED INTO THE ACTIVE SITE, COVALENTLY BOUND TO SER 200 IN A TETRAHEDRAL INTERMEDIATE CONFORMATION. THE ...Details: THE NATURAL SUBSTRATE ACETYLCHOLINE, IN AN ALL-TRANS CONFORMATION, HAS BEEN MANUALLY DOCKED INTO THE ACTIVE SITE, COVALENTLY BOUND TO SER 200 IN A TETRAHEDRAL INTERMEDIATE CONFORMATION. THE ACETYLCHOLINE IS A MODEL, NOT DERIVED FROM THE EXPERIMENTAL DATA.
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.025
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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