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Yorodumi- PDB-1e66: STRUCTURE OF ACETYLCHOLINESTERASE COMPLEXED WITH (-)-HUPRINE X AT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+66 | |||||||||
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Title | STRUCTURE OF ACETYLCHOLINESTERASE COMPLEXED WITH (-)-HUPRINE X AT 2.1A RESOLUTION | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / CHOLINESTERASE / HUPRINE X / ALZHEIMER'S DISEASE / CHEMICAL HYBRID | |||||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | TORPEDO CALIFORNICA (Pacific electric ray) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Dvir, H. / Harel, M. / Silman, I. / Sussman, J.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: 3D Structure of Torpedo Californica Acetylcholinesterase Complexed with Huprine X at 2. 1 A Resolution: Kinetic and Molecular Dynamic Correlates. Authors: Dvir, H. / Wong, D.M. / Harel, M. / Barril, X. / Orozco, M. / Luque, F.J. / Munoz-Torrero, D. / Camps, P. / Rosenberry, T.L. / Silman, I. / Sussman, J.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e66.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e66.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e66_validation.pdf.gz | 761.8 KB | Display | wwPDB validaton report |
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Full document | 1e66_full_validation.pdf.gz | 777.3 KB | Display | |
Data in XML | 1e66_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 1e66_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/1e66 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/1e66 | HTTPS FTP |
-Related structure data
Related structure data | 2aceS S: Starting model for refinement |
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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: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SYNTHETIC HYBRID, HUPRINE X, BOUND AT THE BOTTOM OF THE ACTIVE SITE GORGE Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray) Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase | ||||||
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#2: Sugar | #3: Chemical | ChemComp-HUX / | #4: Water | ChemComp-HOH / | Compound details | HYDROLYZES CHOLINE RELEASED INTO THE SYNAPSE. CATALYTIC ACTIVITY: ACETYLCHOLINE + H(2)O = CHOLINE + ...HYDROLYZES | |
-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: 5.6 Details: PROTEIN WAS CRYSTALLISED FROM 35-40% W/V PEG 200 0.3M MES PH 5.6 4 DEG. CELSIUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.42 Å / Num. obs: 60094 / % possible obs: 76 % / Redundancy: 11.6 % / Biso Wilson estimate: 9.2 Å2 / Rsym value: 0.061 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.52 % / Mean I/σ(I) obs: 2.24 / Rsym value: 0.27 / % possible all: 17.6 |
Reflection | *PLUS Num. all: 60094 / Num. obs: 45140 / Num. measured all: 482340 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 20 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ACE Resolution: 2.1→29.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2910778.11 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: PROLINE 485 IS OUT OF THE 3FO-2FC DENSITY MAP. THE CONSERVED WATER MOLECULE THAT BELONGS TO THE OXYANION HOLE (HOH 682 IN 2ACE NUMBERING) IS ABSENT IN THIS ENTRY ALTHOUGH A POSITIVE ...Details: PROLINE 485 IS OUT OF THE 3FO-2FC DENSITY MAP. THE CONSERVED WATER MOLECULE THAT BELONGS TO THE OXYANION HOLE (HOH 682 IN 2ACE NUMBERING) IS ABSENT IN THIS ENTRY ALTHOUGH A POSITIVE DIFFERENCE DENSITY HAD BEEN DETECTED IN THAT LOCATION. HERE THIS WATER WAS NOT MODELED BECAUSE OF INSUFICIENT SPACE FOR IT DUE TO MOVEMENT OF SER 200.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.6596 Å2 / ksol: 0.345552 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Rfactor obs: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.235 |