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- PDB-3dl4: Non-Aged Form of Mouse Acetylcholinesterase Inhibited by Tabun- Update -

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Basic information

Entry
Database: PDB / ID: 3dl4
TitleNon-Aged Form of Mouse Acetylcholinesterase Inhibited by Tabun- Update
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / tabun / organophosphate / aging / Alternative splicing / Cell junction / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Neurotransmitter degradation / Secreted / Serine esterase / Synapse
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 / laminin binding / side of membrane / synaptic cleft / 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
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsCarletti, E. / Li, H. / Li, B. / Ekstrom, F. / Nicolet, Y. / Loiodice, M. / Gillon, E. / Froment, M.T. / Lockridge, O. / Schopfer, L.M. ...Carletti, E. / Li, H. / Li, B. / Ekstrom, F. / Nicolet, Y. / Loiodice, M. / Gillon, E. / Froment, M.T. / Lockridge, O. / Schopfer, L.M. / Masson, P. / Nachon, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Aging of Cholinesterases Phosphylated by Tabun Proceeds through O-Dealkylation.
Authors: Carletti, E. / Li, H. / Li, B. / Ekstrom, F. / Nicolet, Y. / Loiodice, M. / Gillon, E. / Froment, M.T. / Lockridge, O. / Schopfer, L.M. / Masson, P. / Nachon, F.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 31, 2021Group: Derived calculations / Category: struct_conn / struct_site
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0213
Polymers120,7382
Non-polymers2821
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-9 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.620, 112.940, 226.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 60369.086 Da / Num. of mol.: 2 / Fragment: UNP residues 32-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Plasmid: pcDNA3.1 / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: P21836, acetylcholinesterase
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE C-TERMINAL PART WAS ENGINEERED TO GET MONOMERIC ENZYME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27-31 % (V/V) PEG750MME, 0.1M HEPES, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.06276 Å
DetectorType: MAR CCD / Detector: CCD / Date: Mar 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06276 Å / Relative weight: 1
ReflectionResolution: 2.5→29.2 Å / Num. obs: 71021 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.17 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.856 / SU B: 7.205 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1422 2 %RANDOM
Rwork0.193 ---
obs0.194 70962 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 97.85 Å2 / Biso mean: 46.688 Å2 / Biso min: 21.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8460 0 19 252 8731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228759
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.96111980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48251093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76422.889405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.333151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1181575
X-RAY DIFFRACTIONr_chiral_restr0.1050.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226917
X-RAY DIFFRACTIONr_mcbond_it0.8241.55400
X-RAY DIFFRACTIONr_mcangle_it1.57128709
X-RAY DIFFRACTIONr_scbond_it2.16733359
X-RAY DIFFRACTIONr_scangle_it3.6034.53261
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 105 -
Rwork0.306 5060 -
all-5165 -
obs--100 %

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