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- PDB-2jez: Mus musculus acetylcholinesterase in complex with tabun and HLo-7 -

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Basic information

Entry
Database: PDB / ID: 2jez
TitleMus musculus acetylcholinesterase in complex with tabun and HLo-7
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / MUS MUSCULUS / GLYCOPROTEIN / SERINE ESTERASE / OXIME / MOUSE / HLO-7 / TABUN / SYNAPSE / MEMBRANE
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / positive regulation of dendrite morphogenesis / cholinesterase activity / choline metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway ...acetylcholine metabolic process / serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / positive regulation of dendrite morphogenesis / cholinesterase activity / choline metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / neuromuscular junction / receptor internalization / response to insulin / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / membrane raft / endoplasmic reticulum lumen / hydrolase activity / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / 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
Chem-HLO / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEkstrom, F. / Astot, C. / Pang, Y.P.
CitationJournal: Clin.Pharmacol.Ther. / Year: 2007
Title: Novel Nerve-Agent Antidote Design Based on Crystallographic and Mass Spectrometric Analyses of Tabun-Conjugated Acetylcholinesterase in Complex with Antidotes.
Authors: Ekstrom, F.J. / Astot, C. / Pang, Y.
History
DepositionJan 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 12, 2021Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)121,6835
Polymers120,7382
Non-polymers9453
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint0 kcal/mol
Surface area34830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.920, 108.940, 220.320
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: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
References: UniProt: P21836, acetylcholinesterase, carboxylesterase
#2: Chemical ChemComp-HLO / 1-[({2,4-BIS[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]-4-CARBAMOYLPYRIDINIUM


Mass: 331.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


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


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 3.8 Å3/Da / Density % sol: 70 %
Crystal growpH: 7 / Details: 27-30 % PEG750MME, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.08191
DetectorType: MARRESERACH / Detector: CCD / Date: Oct 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08191 Å / Relative weight: 1
ReflectionResolution: 2.6→29.14 Å / Num. obs: 57837 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.6→29.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.622 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TABUN REACTION PRODUCT COVALENTELY ATTACHED TO SER203.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1144 2 %RANDOM
Rwork0.192 ---
obs0.193 56619 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 67 294 8713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.96611833
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67851060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08722.861395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6831572
X-RAY DIFFRACTIONr_chiral_restr0.0910.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026836
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.26364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.26154
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2785
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6851.55387
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21628576
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.56433715
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6154.53257
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 85 -
Rwork0.267 4113 -
obs--99.98 %

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