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- PDB-1oce: ACETYLCHOLINESTERASE (E.C. 3.1.1.7) COMPLEXED WITH MF268 -

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Basic information

Entry
Database: PDB / ID: 1oce
TitleACETYLCHOLINESTERASE (E.C. 3.1.1.7) COMPLEXED WITH MF268
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / CARBOXYLIC ESTERASE / NEUROTRANSMITTER CLEAVAGE / SERINE ESTERASE
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
CIS-2,6-DIMETHYLMORPHOLINOOCTYLCARBAMYLESEROLINE / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBartolucci, C. / Perola, E. / Cellai, L. / Brufani, M. / Lamba, D.
Citation
Journal: Biochemistry / Year: 1999
Title: "Back door" opening implied by the crystal structure of a carbamoylated acetylcholinesterase.
Authors: Bartolucci, C. / Perola, E. / Cellai, L. / Brufani, M. / Lamba, D.
#1: Journal: Biochim.Biophys.Acta / Year: 1997
Title: Long Chain Analogs of Physostigmine as Potential Drugs for Alzheimer'S Disease: New Insights Into the Mechanism of Action in the Inhibition of Acetylcholinesterase
Authors: Perola, E. / Cellai, L. / Lamba, D. / Filocamo, L. / Brufani, M.
#2: Journal: J.Neurosci.Res. / Year: 1996
Title: Effects of Mf-268, a New Cholinesterase Inhibitor, on Acetylcholine and Biogenic Amines in Rat Cortex
Authors: Zhu, X.D. / Cuadra, G. / Brufani, M. / Maggi, T. / Pagella, P.G. / Williams, E. / Giacobini, E.
#3: Journal: Bioorg.Med.Chem.Lett. / Year: 1995
Title: Synthesis and Structure-Activity Relationships of New Acetylcholinesterase Inhibitors: Morpholinoalkylcarbamoyloxyeseroline Derivatives
Authors: Alisi, M.A. / Brufani, M. / Filocamo, L. / Gostoli, G. / Licandro, E. / Cesta, M.C. / Lappa, S. / Marchesini, D. / Pagella, P.
#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.
History
DepositionJun 12, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 2, 2021Group: Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Advisory / Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)61,0072
Polymers60,7371
Non-polymers2701
Water2,828157
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0144
Polymers121,4732
Non-polymers5412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3240 Å2
ΔGint-12 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.496, 111.496, 137.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ACETYLCHOLINESTERASE


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: INTER-MONOMER DISULFIDE BRIDGE
Source: (natural) Torpedo californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-MF2 / CIS-2,6-DIMETHYLMORPHOLINOOCTYLCARBAMYLESEROLINE / MF268


Mass: 270.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.98 Å3/Da / Density % sol: 68.8 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Sussman, J.L., (1988) J. Mol. Biol., 203, 821.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 %PEG2001reservoir
28-10 mg/mlprotein1drop
318 %PEG2001drop
40.5 MMES1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jun 1, 1997 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 24049 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 42.2 Å2 / Rsym value: 0.14 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.648 / % possible all: 69.7
Reflection
*PLUS
Num. measured all: 248837 / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
% possible obs: 69.7 % / Num. unique obs: 1886 / Rmerge(I) obs: 0.648

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Processing

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

2ace


Resolution: 2.7→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1096 4.9 %RANDOM
Rwork0.208 ---
obs0.208 22426 84.7 %-
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20.43 Å20 Å2
2--2.23 Å20 Å2
3----4.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 19 157 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.591.5
X-RAY DIFFRACTIONx_mcangle_it2.552
X-RAY DIFFRACTIONx_scbond_it2.282
X-RAY DIFFRACTIONx_scangle_it3.332.5
LS refinement shellResolution: 2.7→2.86 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 148 4.8 %
Rwork0.327 2913 -
obs--70.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.63

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