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- PDB-5dti: Crystal structure of mouse acetylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 5dti
TitleCrystal structure of mouse acetylcholinesterase
ComponentsAcetylcholinesterase
KeywordsHYDROLASE
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / 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 ...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: 2.003 Å
AuthorsTran, T.H. / Tong, L.
CitationJournal: Chembiochem / Year: 2015
Title: Discovery of New Classes of Compounds that Reactivate Acetylcholinesterase Inhibited by Organophosphates.
Authors: Katz, F.S. / Pecic, S. / Tran, T.H. / Trakht, I. / Schneider, L. / Zhu, Z. / Ton-That, L. / Luzac, M. / Zlatanic, V. / Damera, S. / Macdonald, J. / Landry, D.W. / Tong, L. / Stojanovic, M.N.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Source and taxonomy
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase


Theoretical massNumber of molelcules
Total (without water)120,0142
Polymers120,0142
Non-polymers00
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-11 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.411, 113.135, 227.199
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: 60006.785 Da / Num. of mol.: 2 / Fragment: UNP residues 32-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell (production host): Hi-5 insect cells by C-PERL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21836, acetylcholinesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% v/v PEG 600, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 126503 / % possible obs: 93 % / Redundancy: 4.6 % / Net I/σ(I): 27.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HA2

2ha2


Resolution: 2.003→45.999 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1998 1.58 %RANDOM
Rwork0.197 ---
obs0.1974 126222 92.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.003→45.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8349 0 0 518 8867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058603
X-RAY DIFFRACTIONf_angle_d0.98111747
X-RAY DIFFRACTIONf_dihedral_angle_d13.5673097
X-RAY DIFFRACTIONf_chiral_restr0.0381263
X-RAY DIFFRACTIONf_plane_restr0.0051549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05310.3611900.29525552X-RAY DIFFRACTION59
2.0531-2.10860.27881060.27856614X-RAY DIFFRACTION70
2.1086-2.17060.30921200.27017497X-RAY DIFFRACTION79
2.1706-2.24070.30591400.25158663X-RAY DIFFRACTION91
2.2407-2.32080.28351500.23519393X-RAY DIFFRACTION99
2.3208-2.41370.24331530.22799490X-RAY DIFFRACTION100
2.4137-2.52350.27021540.21679504X-RAY DIFFRACTION100
2.5235-2.65650.23991510.21529499X-RAY DIFFRACTION100
2.6565-2.8230.24661550.21699563X-RAY DIFFRACTION100
2.823-3.04090.25541540.21819557X-RAY DIFFRACTION100
3.0409-3.34680.24711540.22229591X-RAY DIFFRACTION100
3.3468-3.83090.20961550.19099641X-RAY DIFFRACTION100
3.8309-4.82570.16731560.15289699X-RAY DIFFRACTION100
4.8257-46.01120.19491600.16639961X-RAY DIFFRACTION99

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