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- PDB-1ea5: NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNI... -

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Basic information

Entry
Database: PDB / ID: 1ea5
TitleNATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA at 1.8A resolution
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SERINE HYDROLASE / NEUROTRANSMITTER CLEAVAGE / CATALYTIC TRIAD / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / 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 ...Acetylcholinesterase, fish/snake / 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 speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHarel, M. / Weik, M. / Silman, I. / Sussman, J.L.
Citation
Journal: Biochemistry / Year: 2002
Title: X-Ray Structures of Torpedo Californica Acetylcholinesterase Complexed with (+)-Huperzine a and (-)-Huperzine B: Structural Evidence for an Active Site Rearrangement
Authors: Dvir, H. / Jiang, H.L. / Wong, D.M. / Harel, M. / Chetrit, M. / He, X.C. / Jin, G.Y. / Yu, G.L. / Tang, X.C. / Silman, I. / Bai, D.L. / Sussman, J.L.
#1: Journal: Biochim.Biophys.Acta / Year: 1996
Title: Residues in Torpedo Californica Acetylcholinesterase Necessary for Processing to a Glycosyl Phosphatidylinositol-Anchored Form
Authors: Bucht, G. / Hjalmarsson, K.
#2: Journal: Protein Sci. / Year: 1994
Title: Structure and Dynamics of the Active Site Gorge of Acetylcholinesterase: Synergistic Use of Molecular Dynamics Simulation and X-Ray Crystallography
Authors: Axelsen, P.H. / Harel, M. / Silman, I. / Sussman, J.L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase
Authors: Harel, M. / Schalk, I. / Ehret-Sabatier, L. / Bouet, F. / Goeldner, M. / Hirth, C. / Axelsen, P.H. / Silman, I. / Sussman, J.L.
#4: Journal: Science / Year: 1991
Title: Atomic Structure of Acetylcholinesterase from Torpedo Californica: A Prototypic Acetylcholine-Binding Protein
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I.
#5: Journal: J.Mol.Biol. / Year: 1988
Title: Purification and Crystallization of a Dimeric Form of Acetylcholinesterase from Torpedo Californica Subsequent to Solubilization with Phosphatidylinositol-Specific Phospholipase C
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Varon, L. / Toker, L. / Futerman, A.H. / Silman, I.
#6: Journal: Nature / Year: 1986
Title: Primary Structure of Torpedo Californica Acetylcholinesterase Deduced from its Cdna Sequence
Authors: Schumacher, M. / Camp, S. / Maulet, Y. / Newton, M. / Macphee-Quigley, K. / Taylor, S.S. / Friedmann, T. / Taylor, P.
History
DepositionNov 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Apr 3, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _atom_site.occupancy / _exptl_crystal_grow.temp ..._atom_site.occupancy / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1793
Polymers60,7371
Non-polymers4422
Water13,313739
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3586
Polymers121,4732
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2540 Å2
ΔGint-4.9 kcal/mol
Surface area39100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.573, 111.573, 137.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

DetailsTHE ENZYME IS A GPI-ANCHORED DIMER, THE TWO MONOMERS IN THE DIMER ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY.

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Components

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, 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.: 2
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYZES CHOLINE RELEASED INTO THE SYNAPSE. CATALYTIC ACTIVITY: ACETYLCHOLINE + H(2)O = CHOLINE + ...HYDROLYZES CHOLINE RELEASED INTO THE SYNAPSE. CATALYTIC ACTIVITY: ACETYLCHOLINE + H(2)O = CHOLINE + ACETATE. INHIBITORS OF THE ENZYME ACETYLCHOLINESTERASE (ACHE) SLOW AND SOMETIMES REVERSE THE COGNITIVE DECLINE EXPERIENCED BY INDIVIDUALS WITH ALZHEIMER'S DISEASE. TORPEDO CALIFONICA ACETYLCHOLINESTERASE IS A G2 DIMER IN SOLUTION (SEE SUSSMAN 1988). THE ASYMMETRIC UNIT CONTAINS A MONOMER, WITH THE CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING THE TWO MONOMERS IN A DIMER. THIS IS THE HIGHEST RESOLUTION ACETYLCHLINESTERASE DETERMINED SO FAR. THERE IS RECENT EVIDENCE (SEE BUCHT 1996) THAT THE GPI ANCHOR IS ATTACHED TO EITHER SER 543 OR SER 544, NOT TO CYS 537.

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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: 68 %
Crystal growTemperature: 277 K / pH: 5.8
Details: PROTEIN WAS CRYSTALLIZED FROM 35% PEG 200, 100 MM MES, PH 5.8, AT 4 DEG.

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Data collection

DiffractionMean temperature: 155 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9312
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9312 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 86444 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.251 / % possible all: 68.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Resolution: 1.8→27.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1738173.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE THREE N- TERMINAL RESIDUES (ASP 1, ASP 2, HIS 3), AND THE C-TERMINAL RESIDUES AFTER THR 535. THERE ARE ...Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE THREE N- TERMINAL RESIDUES (ASP 1, ASP 2, HIS 3), AND THE C-TERMINAL RESIDUES AFTER THR 535. THERE ARE 2 ALTERNATE CONFORMATIONS OBSERVED FOR RESIDUES: 9, 16, 19, 24, 46, 49, 55, 65, 221, 228, 260, 344, 353, 408, 430, 455, 468, 478, 508, 526.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4317 5 %RANDOM
Rwork0.185 ---
obs0.185 86179 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.8547 Å2 / ksol: 0.367212 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.58 Å22.62 Å20 Å2
2--6.58 Å20 Å2
3----13.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a0.22 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 28 739 4985
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 597 5.1 %
Rwork0.289 11185 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMCARBOHYDRATE.TOP

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