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- PDB-5ov9: Crystal structure of Acetylcholinesterase in complex with Crystal... -

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Basic information

Entry
Database: PDB / ID: 5ov9
TitleCrystal structure of Acetylcholinesterase in complex with Crystal Violet
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Dimeric / complex / inhibitor
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / 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, catalytic domain ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / 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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / CRYSTAL VIOLET / 2-ETHOXYETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsAllgardsson, A. / Andersson, C.D. / Akfur, C. / Worek, F. / Linusson, A. / Ekstrom, F.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2014-4675 Sweden
Swedish Ministry of Defence Sweden
CitationJournal: Molecules / Year: 2017
Title: An Unusual Dimeric Inhibitor of Acetylcholinesterase: Cooperative Binding of Crystal Violet.
Authors: Allgardsson, A. / David Andersson, C. / Akfur, C. / Worek, F. / Linusson, A. / Ekstrom, F.
History
DepositionAug 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _chem_comp.pdbx_synonyms
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,90421
Polymers120,4682
Non-polymers3,43619
Water9,782543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.630, 113.890, 226.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Acetylcholinesterase / / AChE


Mass: 60233.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment: CATALYTIC DOMAIN, UNP RESIDUES 32-574 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 , 9 types, 560 molecules

#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CVI / CRYSTAL VIOLET / Crystal violet


Mass: 372.526 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H30N3 / Comment: antifungal, antibiotic*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL / 2-(2-Ethoxyethoxy)ethanol


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#10: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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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: 4.35 Å3/Da / Density % sol: 71.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 30% (v/v) polyethylene glycol 750 monomethylether, 100 mM HEPES, pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.03805 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03805 Å / Relative weight: 1
ReflectionResolution: 2.4→29.106 Å / Num. obs: 80635 / % possible obs: 98.22 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.04764 / Rrim(I) all: 0.0545 / Net I/σ(I): 16.39
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4941 / Num. measured obs: 32579 / Num. unique all: 7919 / Rrim(I) all: 0.5644

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.4→29.106 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.64 / Details: TLS was used in refinement
RfactorNum. reflection% reflection
Rfree0.1953 1585 1.98 %
Rwork0.1586 --
obs0.1593 79973 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 388.22 Å2 / Biso mean: 54.7852 Å2 / Biso min: 25.89 Å2
Refinement stepCycle: final / Resolution: 2.4→29.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8282 0 238 543 9063
Biso mean--80.09 53.54 -
Num. residues----1065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128842
X-RAY DIFFRACTIONf_angle_d1.36412042
X-RAY DIFFRACTIONf_chiral_restr0.0561274
X-RAY DIFFRACTIONf_plane_restr0.0071588
X-RAY DIFFRACTIONf_dihedral_angle_d17.0053147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47740.26881340.22687018715298
2.4774-2.56590.27661280.20297033716198
2.5659-2.66860.23751600.19237015717598
2.6686-2.790.23471510.19037063721499
2.79-2.93690.28261440.19627096724099
2.9369-3.12070.23351540.18847118727299
3.1207-3.36140.19531460.1787168731499
3.3614-3.6990.18571380.15877222736099
3.699-4.23290.16311380.13327209734799
4.2329-5.32760.14841470.12057191733898
5.3276-29.10790.18291450.15047255740095
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13270.1251-0.35331.0544-0.4372.5923-0.0537-0.1471-0.01530.12950.0272-0.050.0395-0.00850.01960.29060.0271-0.00230.2840.03930.333331.730311.744328.5607
22.80351.54470.36952.65530.43133.88370.00040.28990.0289-0.2174-0.1086-0.1478-0.05910.50840.1060.34690.05530.04020.41390.08780.371148.400816.849710.1963
35.0009-0.664-0.00561.5451-0.2322.6353-0.21470.1333-0.5953-0.07030.1495-0.01010.50950.05930.0580.4539-0.04010.01420.3249-0.02950.286428.59544.76379.9861
41.1062-0.2011-0.40891.0129-0.53763.5185-0.04830.1004-0.0085-0.13390.03880.1073-0.0378-0.3351-0.01390.3011-0.0413-0.04940.38030.00750.385219.11117.6896.5081
54.34010.21761.04482.7214-2.26396.6924-0.084-0.0823-0.691-0.01360.02420.75990.8307-1.2916-0.02310.4597-0.18080.03050.56760.03380.49717.7971.982913.8031
60.5893-0.2920.0942.50890.74091.96330.0420.2849-0.162-0.3008-0.08150.10430.2151-0.143-0.02930.4944-0.0424-0.12260.56840.02620.341618.03668.6224-0.661
75.0565-0.8831-1.47742.02740.4613.47950.09580.3614-0.0162-0.2588-0.24720.3146-0.1865-0.41630.09310.42730.0834-0.08880.5371-0.16560.3989-2.97155.938-61.2625
81.0681-0.38540.52641.44660.122.87760.13410.1041-0.2601-0.058-0.25740.13180.4618-0.16040.02420.449-0.0182-0.02890.4614-0.11580.3874.9446-4.3623-52.7334
92.5002-0.0830.12151.48290.77531.82410.11140.2052-0.0239-0.1313-0.36320.5147-0.0457-0.55460.13940.3180.0387-0.06260.4907-0.1250.4098-1.22754.7-50.2457
103.8439-2.15111.99323.3972-1.05051.86630.13770.09790.1405-0.194-0.1458-0.0592-0.06470.11160.02760.37710.0348-0.00390.3926-0.08750.296511.70596.8977-53.5212
111.8555-1.07170.07662.82190.82492.420.0835-0.05980.00620.09950.0412-0.22030.24940.3455-0.10010.34640.006-0.02170.419-0.05290.335318.91172.9222-44.6568
121.9269-1.12521.08042.9231-0.1993.57070.2093-0.15-0.29850.3759-0.02270.15460.6491-0.1104-0.18520.5157-0.04920.02340.3426-0.07120.383110.3815-0.6722-26.4705
135.40932.0956-0.82692.2963-0.67494.69010.1742-0.5945-0.15990.3029-0.05380.04130.5169-0.0113-0.13430.6834-0.0624-0.04630.4516-0.04130.420215.7313-1.4066-16.4868
142.16180.16730.15952.71770.24322.78970.1373-0.09150.00670.1276-0.16850.43340.2132-0.44820.03670.3697-0.0480.05930.4729-0.13010.4046-2.15498.7259-33.0225
153.24532.72230.36016.0013-0.87846.3927-0.0261-0.33650.44950.13850.10680.4116-0.4693-0.39980.04890.46670.02780.02860.4483-0.12420.4996-0.390722.6412-28.6755
161.489-0.10541.20392.003-0.1280.9705-0.24160.22260.43040.38720.00480.0147-0.0880.2930.28960.5837-0.05340.0680.5382-0.05940.246312.0110.6096-21.3183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 237 )A1 - 237
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 300 )A238 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 341 )A301 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 486 )A342 - 486
5X-RAY DIFFRACTION5chain 'A' and (resid 487 through 513 )A487 - 513
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 541 )A514 - 541
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 45 )B4 - 45
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 86 )B46 - 86
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 141 )B87 - 141
10X-RAY DIFFRACTION10chain 'B' and (resid 142 through 190 )B142 - 190
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 318 )B191 - 318
12X-RAY DIFFRACTION12chain 'B' and (resid 319 through 366 )B319 - 366
13X-RAY DIFFRACTION13chain 'B' and (resid 367 through 406 )B367 - 406
14X-RAY DIFFRACTION14chain 'B' and (resid 407 through 486 )B407 - 486
15X-RAY DIFFRACTION15chain 'B' and (resid 487 through 513 )B487 - 513
16X-RAY DIFFRACTION16chain 'B' and (resid 514 through 541 )B514 - 541

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