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- PDB-1eea: Acetylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 1eea
TitleAcetylcholinesterase
ComponentsPROTEIN (ACETYLCHOLINESTERASE)
KeywordsHYDROLASE / SERINE HYDROLASE / ALPHA/BETA HYDROLASE / TETRAMER
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, 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
Similarity search - Domain/homology
Acetylcholinesterase
Similarity search - Component
Biological speciesElectrophorus electricus (electric eel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsRaves, M.L. / Giles, K. / Schrag, J.D. / Schmid, M.F. / Phillips Jr., G.N. / Wah, C. / Howard, A.J. / Silman, I. / Sussman, J.L.
Citation
Journal: Structure and Function of Cholinesterases and Related Proteins
Year: 1998
Title: Quaternary Structure of Tetrameric Acetylcholinesterase
Authors: Raves, M.L. / Giles, K. / Schrag, J.D. / Schmid, M.F. / Phillips Jr., G.N. / Wah, C. / Howard, A.J. / Silman, I. / Sussman, J.L. / Doctor, B.P. / Quinn, D.M. / Rotundo, R.L. / Taylor, P.
#1: Journal: Protein Eng. / Year: 1997
Title: Interactions underlying subunit association in cholinesterases.
Authors: Giles, K.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Crystallization and preliminary X-ray diffraction analysis of 11 S acetylcholinesterase.
Authors: Schrag, J.D. / Schmid, M.F. / Morgan, D.G. / Phillips Jr., G.N. / Chiu, W. / Tang, L.
History
DepositionJan 26, 1999Processing site: RCSB
Revision 1.0Feb 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 21, 2014Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author / citation_editor
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.6Dec 18, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.7Aug 9, 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
Revision 1.8Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ACETYLCHOLINESTERASE)


Theoretical massNumber of molelcules
Total (without water)60,4611
Polymers60,4611
Non-polymers00
Water00
1
A: PROTEIN (ACETYLCHOLINESTERASE)

A: PROTEIN (ACETYLCHOLINESTERASE)


Theoretical massNumber of molelcules
Total (without water)120,9222
Polymers120,9222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1740 Å2
ΔGint-17 kcal/mol
Surface area36470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.860, 201.460, 235.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein PROTEIN (ACETYLCHOLINESTERASE)


Mass: 60461.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: SEE REMARK 450 FOR INFORMATION REGARDING THE SOURCE AND SEQUENCE
Source: (natural) Electrophorus electricus (electric eel) / Organ: ELECTRIC ORGAN / Variant: G4 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
Has protein modificationY
Source detailsTHE SEQUENCE LISTED IN THE SEQRES RECORD IS OF TORPEDO CALIFORNICA ACETYLCHOLINESTERASE, ...THE SEQUENCE LISTED IN THE SEQRES RECORD IS OF TORPEDO CALIFORNICA ACETYLCHOLINESTERASE, (CORRESPONDING TO THE STRUCTURE) NOT OF ELECTROPHORUS ELECTRICUS. AT THE RESOLUTION OF THE EXPERIMENTAL DATA (4.5 A) NO SEQUENCE DISCREPANCIES CAN BE SEEN

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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: 6.5 Å3/Da / Density % sol: 81 %
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jan 15, 1987
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4.5→34.3 Å / Num. obs: 9717 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.7
Reflection shellResolution: 4.5→4.65 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2 / % possible all: 75.2

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Highest resolution: 4.5 Å
Details: NO REFINEMENT WAS CARRIED OUT ON THE MODEL. FINAL MODEL IS MOLECULAR REPLACEMENT SOLUTION FOR SEARCH MODEL 2ACE. ONLY ONE MONOMER WAS FOUND TO OCCUPY THE ASYMMETRIC UNIT. THE FULL PACKING OF ...Details: NO REFINEMENT WAS CARRIED OUT ON THE MODEL. FINAL MODEL IS MOLECULAR REPLACEMENT SOLUTION FOR SEARCH MODEL 2ACE. ONLY ONE MONOMER WAS FOUND TO OCCUPY THE ASYMMETRIC UNIT. THE FULL PACKING OF THE UNIT CELL (16 MONOMERS, 4 TETRAMERS) SHOWS LARGE VOIDS THAT COULD EASILY BE OCCUPIED BY FOUR MORE TETRAMERS BY SIMPLE TRANSLATION OF THE OBTAINED TETRAMERS BY HALF THE C AXIS. REFINEMENT DOES NOT AGREE WITH TWO MONOMERS IN THE ASYMMETRIC UNIT.
Refinement stepCycle: LAST / Highest resolution: 4.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 0 0 4115

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