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- PDB-2ace: NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA -

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Basic information

Entry
Database: PDB / ID: 2ace
TitleNATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA
ComponentsACETYLCHOLINESTERASE
KeywordsSERINE HYDROLASE / NEUROTRANSMITTER CLEAVAGE / CATALYTIC TRIAD / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / 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 ...Acetylcholinesterase, fish/snake / : / 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
ACETYLCHOLINE / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHarel, M. / Raves, M.L. / Silman, I. / Sussman, J.L.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A.
Authors: Raves, M.L. / Harel, M. / Pang, Y.-P. / Silman, I. / Kozikowski, A.P. / 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
DepositionJun 23, 1996Processing site: BNL
SupersessionNov 8, 1996ID: 1ACE
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 22, 2016Group: Derived calculations
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8832
Polymers60,7371
Non-polymers1461
Water3,675204
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7654
Polymers121,4732
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2770 Å2
ΔGint1 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.410, 112.410, 136.700
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-732-

HOH

DetailsTORPEDO 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.

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Components

#1: Protein ACETYLCHOLINESTERASE


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: Chemical ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS RECENT EVIDENCE (SEE BUCHT 1996) THAT THE GPI ANCHOR IS ATTACHED TO EITHER SER 543 OR SER ...THERE IS RECENT EVIDENCE (SEE BUCHT 1996) THAT THE GPI ANCHOR IS ATTACHED TO EITHER SER 543 OR SER 544, NOT TO CYS 537.
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: 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., temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
138 %PEG2001reservoir
20.1 MMES1reservoir
312 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 46243 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.095 / Net I/σ(I): 7.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.9 / Rsym value: 0.713 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 138332 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.621

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACE

1ace
PDB Unreleased entry


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE NATURAL SUBSTRATE ACETYLCHOLINE, IN AN ALL-TRANS CONFORMATION, HAS BEEN MANUALLY DOCKED INTO THE ACTIVE SITE, COVALENTLY BOUND TO SER 200 IN A TETRAHEDRAL INTERMEDIATE CONFORMATION. THE ...Details: THE NATURAL SUBSTRATE ACETYLCHOLINE, IN AN ALL-TRANS CONFORMATION, HAS BEEN MANUALLY DOCKED INTO THE ACTIVE SITE, COVALENTLY BOUND TO SER 200 IN A TETRAHEDRAL INTERMEDIATE CONFORMATION. THE ACETYLCHOLINE IS A MODEL, NOT DERIVED FROM THE EXPERIMENTAL DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1555 5.2 %RANDOM
Rwork0.199 ---
obs0.199 30035 96.6 %-
Displacement parametersBiso mean: 24.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a-0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 10 204 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.411.5
X-RAY DIFFRACTIONx_mcangle_it2.262
X-RAY DIFFRACTIONx_scbond_it2.092
X-RAY DIFFRACTIONx_scangle_it3.122.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.39 167 5.2 %
Rwork0.308 3181 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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