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Yorodumi- PDB-2wg2: NON-AGED CONJUGATE OF TORPEDO CALIFORNICA ACETYLCHOLINESTERASE WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wg2 | |||||||||
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Title | NON-AGED CONJUGATE OF TORPEDO CALIFORNICA ACETYLCHOLINESTERASE WITH SOMAN (ALTERNATIVE REFINEMENT) | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / AGING / CELL MEMBRANE / NEUROTRANSMITTER DEGRADATION / SYNAPSE MEMBRANE / ALZHEIMER DISEASE / GPI-ANCHOR / GLYCOPROTEIN / CELL JUNCTION | |||||||||
Function / homology | Function and homology information acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / 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: 1.95 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wg2.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wg2.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wg2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2wg2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2wg2_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 2wg2_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wg2 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wg2 | HTTPS FTP |
-Related structure data
Related structure data | 2wfzC 2wg0C 2wg1C 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 , 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 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: 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 |
-Non-polymers , 6 types, 670 molecules
#4: Chemical | ChemComp-GD8 / ( | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-PG4 / #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-CL / | #9: 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 % / Description: NONE |
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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 6 MIN IN 1.3 MM SOMAN AT PH 8, 4 DEG C., THEN FLASH-COOLED IN LN2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.2 Å / Num. obs: 71726 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EA5 Resolution: 1.95→45.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.665 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS MODEL WAS OBTAINED FROM AN ALTERNATIVE REFINEMENT OF THE STRUCTURE OF THE NON-AGED CONJUGATE OF TCACHE WITH SOMAN (PDB ENTRY CODE: ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS MODEL WAS OBTAINED FROM AN ALTERNATIVE REFINEMENT OF THE STRUCTURE OF THE NON-AGED CONJUGATE OF TCACHE WITH SOMAN (PDB ENTRY CODE: 2WFZ). THE RESTRAINTS ON BOTH THE LENGTH OF THE CALPHA-O2 BOND AND THE GEOMETRY OF THE CALPHA ATOM OF THE SOMAN ADDUCT WERE LOOSENED. THIS IS DESCRIBED IN THE SUPPLEMENTARY INFORMATION OF THE PUBLICATION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→45.79 Å
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Refine LS restraints |
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