[English] 日本語
Yorodumi- PDB-2wg0: AGED CONJUGATE OF TORPEDO CALIFORNICA ACETYLCHOLINESTERASE WITH S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wg0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | AGED CONJUGATE OF TORPEDO CALIFORNICA ACETYLCHOLINESTERASE WITH SOMAN (OBTAINED BY IN CRYSTALLO AGING) | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / SOMAN / AGING / SYNAPSE / MEMBRANE / CELL MEMBRANE / DISULFIDE BOND / SERINE ESTERASE / NEUROTRANSMITTER CLEAVAGE / CONFORMATIONAL FLEXIBILITY / NEUROTRANSMITTER DEGRADATION / ALPHA/BETA HYDROLASE / ALTERNATIVE SPLICING / ORGANOPHOSPHATE / SYNAPSE MEMBRANE / ALZHEIMER DISEASE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION | |||||||||
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: 2.2 Å | |||||||||
Authors | Sanson, B. / Nachon, F. / Colletier, J.P. / Froment, M.T. / Toker, L. / Greenblatt, H.M. / Sussman, J.L. / Ashani, Y. / Masson, P. / Silman, I. / Weik, M. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Crystallographic Snapshots of Nonaged and Aged Conjugates of Soman with Acetylcholinesterase, and of a Ternary Complex of the Aged Conjugate with Pralidoxime. Authors: Sanson, B. / Nachon, F. / Colletier, J.P. / Froment, M.T. / Toker, L. / Greenblatt, H.M. / Sussman, J.L. / Ashani, Y. / Masson, P. / Silman, I. / Weik, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wg0.cif.gz | 143 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wg0.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wg0 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wg0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2wfzC 2wg1C 2wg2C 1ea5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-558 / 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 |
---|
-Sugars , 2 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar |
-Non-polymers , 7 types, 638 molecules
#4: Chemical | ChemComp-CL / | ||||
---|---|---|---|---|---|
#5: Chemical | ChemComp-GB / | ||||
#6: Chemical | ChemComp-MES / | ||||
#7: Chemical | ChemComp-PG4 / | ||||
#8: Chemical | ChemComp-PGE / #9: Chemical | ChemComp-PEG / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K / pH: 5.8 Details: ACHE WAS CRYSTALLIZED IN 34% PEG200, 150 MM MES, PH 6, 4 DEG. C. THE CRYSTAL WAS SOAKED FOR 2 HOURS IN 1.3 MM SOMAN AT PH 6, 4 DEG C., THEN FLASH-COOLED IN LN2. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.6 Å / Num. obs: 50212 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.25 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EA5 Resolution: 2.2→48.34 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.787 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 25.416 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|