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- PDB-7b8e: Torpedo californica acetylcholinesterase complexed with Ca+2 -

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Basic information

Entry
Database: PDB / ID: 7b8e
TitleTorpedo californica acetylcholinesterase complexed with Ca+2
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / ASSAM / differential scanning calorimetry / divalent metal ion / electron paramagnetic resonance / thermal inactivation / Torpedo / 4D motif / 3.1.1.7
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
Similarity search - Domain/homology
2-[2-(2-ethoxyethoxy)ethoxy]ethanol / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsSilman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L.
Citation
Journal: Protein Sci. / Year: 2021
Title: Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif.
Authors: Silman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L.
#1: 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.
#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.
History
DepositionDec 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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 1.4Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,21910
Polymers60,7371
Non-polymers1,4839
Water4,468248
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,43920
Polymers121,4732
Non-polymers2,96618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Buried area5690 Å2
ΔGint-32 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.074, 139.074, 71.319
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-919-

HOH

21A-939-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetylcholinesterase / AChE


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetronarce californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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

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Non-polymers , 5 types, 254 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FWN / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: By mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M calcium acetate/10-15% ...Details: By mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M calcium acetate/10-15% (v/v) polyethylene glycol (PEG) 5000 monomethyl ether, 0.1 M MES, pH 6.5), thus yielding crystals of the Ca+2/TcAChE complex.

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Data collection

DiffractionMean temperature: 155 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.23→19.96 Å / Num. obs: 38704 / % possible obs: 99.36 % / Redundancy: 4 % / Biso Wilson estimate: 39.68 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.6
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 3752

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
REFMAC5.8.0258refinement
DENZOv1.0data reduction
SCALEPACKv1.0data scaling
MERLOTv1.0phasing
Coot9.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA5

1ea5


Resolution: 2.23→19.96 Å / SU ML: 0.2692 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 1913 4.94 %
Rwork0.179 36789 -
obs0.1813 38702 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.68 Å2
Refinement stepCycle: LAST / Resolution: 2.23→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 92 248 4566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814456
X-RAY DIFFRACTIONf_angle_d0.87646047
X-RAY DIFFRACTIONf_chiral_restr0.0566647
X-RAY DIFFRACTIONf_plane_restr0.0052783
X-RAY DIFFRACTIONf_dihedral_angle_d3.05043601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.290.31361240.24532490X-RAY DIFFRACTION95.16
2.29-2.350.32711300.23982591X-RAY DIFFRACTION99.93
2.35-2.420.28541440.23432606X-RAY DIFFRACTION99.85
2.42-2.490.28361310.22412616X-RAY DIFFRACTION99.96
2.49-2.580.2711280.21912650X-RAY DIFFRACTION100
2.58-2.690.28761460.20932610X-RAY DIFFRACTION99.89
2.69-2.810.26731340.20952612X-RAY DIFFRACTION99.89
2.81-2.960.2631340.20972639X-RAY DIFFRACTION99.89
2.96-3.140.25991350.20742629X-RAY DIFFRACTION99.86
3.14-3.380.23061450.19892634X-RAY DIFFRACTION99.75
3.38-3.720.21931370.16762636X-RAY DIFFRACTION99.93
3.72-4.250.19111520.15522649X-RAY DIFFRACTION99.89
4.25-5.340.1921240.12972685X-RAY DIFFRACTION99.89
5.34-19.960.17321490.15952742X-RAY DIFFRACTION99.48

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