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- PDB-2ack: ACETYLCHOLINESTERASE COMPLEXED WITH EDROPHONIUM, MONOCHROMATIC DATA -

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Basic information

Entry
Database: PDB / ID: 2ack
TitleACETYLCHOLINESTERASE COMPLEXED WITH EDROPHONIUM, MONOCHROMATIC DATA
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / CARBOXYLIC 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
EDROPHONIUM ION / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRaves, M.L. / Sussman, J.L. / Harel, M. / Silman, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Static Laue diffraction studies on acetylcholinesterase.
Authors: Ravelli, R.B. / Raves, M.L. / Ren, Z. / Bourgeois, D. / Roth, M. / Kroon, J. / Silman, I. / Sussman, J.L.
#1: 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.
#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.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.
History
DepositionOct 29, 1997Processing site: BNL
SupersessionFeb 11, 1998ID: 1ACK
Revision 1.0Feb 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 29, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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)60,9032
Polymers60,7371
Non-polymers1661
Water4,540252
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8064
Polymers121,4732
Non-polymers3322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2870 Å2
ΔGint-1 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.409, 112.409, 136.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
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 / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-EDR / EDROPHONIUM ION


Mass: 166.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.6 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 277 K / pH: 5.8
Details: PROTEIN WAS CRYSTALLISED FROM 40 % PEG200, 100 MM MES, PH 5.8 AT 4 DEGREES C., temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Raves, M.L., (1997) Nature Struct.Biol., 4, 57.
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: 2.4→33.3 Å / Num. obs: 38611 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.089 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.42 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 275832 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.42

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1890 4.9 %RANDOM
obs0.213 38560 97.7 %-
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 12 252 4410
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 38560
Solvent computation
*PLUS
Displacement parameters
*PLUS

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