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Yorodumi- PDB-2y2v: Nonaged form of Mouse Acetylcholinesterase inhibited by sarin-Update -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y2v | |||||||||
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Title | Nonaged form of Mouse Acetylcholinesterase inhibited by sarin-Update | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / CHOLINESTERASE / METHYLPHOSPHONATE | |||||||||
Function / homology | Function and homology information acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Akfur, C. / Artursson, E. / Ekstrom, F. | |||||||||
Citation | Journal: To be Published Title: Methylphosphonate Adducts of Acetylcholinesterase Investigated by Time Correlated Single Photon Counting and X-Ray Crystallography Authors: Akfur, C. / Artursson, E. / Ekstrom, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y2v.cif.gz | 236.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y2v.ent.gz | 188.8 KB | Display | PDB format |
PDBx/mmJSON format | 2y2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y2v_validation.pdf.gz | 846.6 KB | Display | wwPDB validaton report |
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Full document | 2y2v_full_validation.pdf.gz | 863.6 KB | Display | |
Data in XML | 2y2v_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 2y2v_validation.cif.gz | 70.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y2v ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y2v | HTTPS FTP |
-Related structure data
Related structure data | 2y2uC 1j06S C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.735238, -0.403452, -0.545658), Vector: |
-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 60354.070 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 Source method: isolated from a genetically manipulated source Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase #2: Sugar | |
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-Non-polymers , 5 types, 734 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-P15 / | #6: Chemical | ChemComp-ETX / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | RESIDUE SGB REPRESENTS |
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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: 3.9 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 26-30% (V/V) PEG 750MME, 0.1 M HEPES PH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: May 13, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03908 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→29.14 Å / Num. obs: 306983 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 50.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J06 Resolution: 2.45→28.979 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 20.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.816 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.45→28.979 Å
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Refine LS restraints |
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LS refinement shell |
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