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Yorodumi- PDB-1vxo: METHYLPHOSPHONYLATED ACETYLCHOLINESTERASE (AGED) OBTAINED BY REAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vxo | |||||||||
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Title | METHYLPHOSPHONYLATED ACETYLCHOLINESTERASE (AGED) OBTAINED BY REACTION WITH O-ETHYL-S-[2-[BIS(1-METHYLETHYL)AMINO]ETHYL] METHYLPHOSPHONOTHIOATE (VX) | |||||||||
Components | PROTEIN (ACETYLCHOLINESTERASE) | |||||||||
Keywords | HYDROLASE / CHOLINESTERASE / ORGANOPHOSPHATE / SERINE HYDROLASE / CHEMICAL-WARFARE | |||||||||
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: 2.4 Å | |||||||||
Authors | Millard, C.B. / Silman, I. / Sussman, J.L. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1999 Title: Reaction Products of Acetylcholinesterase and VX Reveal a Mobile Histidine in the Catalytic Triad Authors: Millard, C.B. / Koellner, G. / Ordentlich, A. / Shafferman, A. / 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 | 1vxo.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vxo.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vxo_validation.pdf.gz | 403.8 KB | Display | wwPDB validaton report |
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Full document | 1vxo_full_validation.pdf.gz | 411.7 KB | Display | |
Data in XML | 1vxo_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1vxo_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/1vxo ftp://data.pdbj.org/pub/pdb/validation_reports/vx/1vxo | 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: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPLEXED WITH THE NERVE AGENT VX (AGED) Source: (natural) Torpedo californica (Pacific electric ray) Cellular location: MEMBRANE BOUND BY GPI ANCHOR / Organ: ELECTRIC ORGAN / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase | ||||||||
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#2: Sugar | #3: Chemical | ChemComp-VXA / | #4: Water | ChemComp-HOH / | Compound details | ACHE WAS PHOSPHONYLATED WITH VX, THE CONJUGATE WAS CRYSTALLIZED, AND SUBSEQUENTLY ALLOWED TO ...ACHE WAS PHOSPHONYL | Nonpolymer details | ANIONIC METHYLPHOS | |
-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: 6 Details: 35-40% (W/V) PEG-200 0.15 M MES BUFFER PH 6, 0.05 M NACL, pH 6.00, temperature 277.00K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 68 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Millard, C.B., (1999) Biochemistry, 38, 7032. / PH range low: 6 / PH range high: 5.8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Mar 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 38823 / % possible obs: 97.2 % / Redundancy: 10.7 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.24 / % possible all: 80.5 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % possible obs: 97.2 % |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ACE Resolution: 2.4→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1956322.52 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: USED COMPOSITE-OMIT MAP METHOD CONTINUOUS POSITIVE DIFFERENCE DENSITY IN (FO-FC) MAPS OCCURS IN FRONT OF THE INDOLE RINGS OF W84 AND W279. THIS DENSITY IS PRESENTLY MODELED WITH WATERS ...Details: USED COMPOSITE-OMIT MAP METHOD CONTINUOUS POSITIVE DIFFERENCE DENSITY IN (FO-FC) MAPS OCCURS IN FRONT OF THE INDOLE RINGS OF W84 AND W279. THIS DENSITY IS PRESENTLY MODELED WITH WATERS 1074/1075/1077 (W84) AND WATERS 1079/1087/1127/1107 (W279).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.82 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.238 |