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- PDB-3dl7: Aged Form of Mouse Acetylcholinesterase Inhibited by Tabun- Update -

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Basic information

Entry
Database: PDB / ID: 3dl7
TitleAged Form of Mouse Acetylcholinesterase Inhibited by Tabun- Update
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / tabun / organophosphate / aging / 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: Non-polymer description / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4156
Polymers120,6822
Non-polymers7334
Water7,909439
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.020, 110.880, 226.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Acetylcholinesterase / / AChE


Mass: 60341.031 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 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 442 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.11 Å3/Da / Density % sol: 70.06 %
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: 0.9694 Å
DetectorType: MAR CCD / Detector: CCD / Date: Mar 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9694 Å / Relative weight: 1
ReflectionResolution: 2.5→29 Å / Num. obs: 69074 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 7.5 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.892 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1381 2 %RANDOM
Rwork0.187 ---
obs0.188 69037 99.16 %-
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: 110.59 Å2 / Biso mean: 49.689 Å2 / Biso min: 21.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 47 439 8872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228735
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.96311943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47351078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48522.761402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.585151268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0971575
X-RAY DIFFRACTIONr_chiral_restr0.0970.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026867
X-RAY DIFFRACTIONr_nbd_refined0.2180.24609
X-RAY DIFFRACTIONr_nbtor_refined0.3150.26024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2591
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.211
X-RAY DIFFRACTIONr_mcbond_it0.7761.55461
X-RAY DIFFRACTIONr_mcangle_it1.35528661
X-RAY DIFFRACTIONr_scbond_it1.79233713
X-RAY DIFFRACTIONr_scangle_it2.9014.53277
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 104 -
Rwork0.291 4887 -
all-4991 -
obs--98.79 %

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