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Yorodumi- PDB-2v98: Structure of the complex of TcAChE with 1-(2-nitrophenyl)-2,2,2- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v98 | ||||||
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Title | Structure of the complex of TcAChE with 1-(2-nitrophenyl)-2,2,2- trifluoroethyl-arsenocholine after a 9 seconds annealing to room temperature, during the first 5 seconds of which laser irradiation at 266nm took place | ||||||
Components | ACETYLCHOLINESTERASE | ||||||
Keywords | HYDROLASE / PARTIAL Q-WEIGHTED DIFFERENCE REFINEMENT / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE SPLICING / KINETIC CRYSTALLOGRAPHY / SERINE ESTERASE / CAGED COMPOUNDS / ACETYLCHOLINESTERASE / SYNAPSE / MEMBRANE / BACKDOOR / 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: 3 Å | ||||||
Authors | Colletier, J.-P. / Sanson, B. / Royant, A. / Specht, A. / Nachon, F. / Masson, P. / Zaccai, G. / Sussman, J.L. / Goeldner, M. / Silman, I. ...Colletier, J.-P. / Sanson, B. / Royant, A. / Specht, A. / Nachon, F. / Masson, P. / Zaccai, G. / Sussman, J.L. / Goeldner, M. / Silman, I. / Bourgeois, D. / Weik, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Use of a 'Caged' Analog to Study Traffic of Choline within Acetylcholinesterase by Kinetic Crystallography Authors: Colletier, J.-P. / Royant, A. / Specht, A. / Sanson, B. / Nachon, F. / Masson, P. / Zaccai, G. / Sussman, J.L. / Goeldner, M. / Silman, I. / Bourgeois, D. / Weik, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v98.cif.gz | 435.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v98.ent.gz | 374.8 KB | Display | PDB format |
PDBx/mmJSON format | 2v98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v98 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v98 | HTTPS FTP |
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-Related structure data
Related structure data | 2v96C 2v97C 2va9C 1w75S 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
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 2 / 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 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-CFQ / #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6 Details: 32% PEG200, 150MM MES, PH6, 4 DEG. C. THE CRYSTAL WAS SOAKED IN A MOTHER LIQUOR SOLUTION CONTAINING 0.5MM CAGED ARSENOCHOLINE DURING 12 HOURS, IN THE DARK AND AT 4 DEG. C., pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93224 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93224 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 53938 / % possible obs: 96.6 % / Observed criterion σ(I): 2.5 / Redundancy: 3.3 % / Biso Wilson estimate: 47.81 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.84 |
Reflection shell | Resolution: 3→3.17 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W75 Resolution: 3→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3426122.57 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.04135534 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.05 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
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Xplor file |
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