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- PDB-6o50: Binary complex of native hAChE with BW284c51 -

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Basic information

Entry
Database: PDB / ID: 6o50
TitleBinary complex of native hAChE with BW284c51
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / BW284c51
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / positive regulation of protein secretion / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / nervous system development / amyloid-beta binding / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / 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 ...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
Chem-EBW / NITRATE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsGerlits, O. / Kovalevsky, A. / Radic, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1U01NS083451 United States
CitationJournal: Chem.Biol.Interact. / Year: 2019
Title: A new crystal form of human acetylcholinesterase for exploratory room-temperature crystallography studies.
Authors: Gerlits, O. / Ho, K.Y. / Cheng, X. / Blumenthal, D. / Taylor, P. / Kovalevsky, A. / Radic, Z.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 19, 2020Group: 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
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value
Revision 1.4Oct 11, 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 1.5Oct 16, 2024Group: Structure summary / Category: 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
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8209
Polymers120,5762
Non-polymers1,2447
Water3,909217
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8209
Polymers120,5762
Non-polymers1,2447
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+y+1,-x,z-1/31
Buried area5110 Å2
ΔGint-18 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.180, 125.180, 130.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60287.977 Da / Num. of mol.: 2 / Fragment: residues 32-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Chemical ChemComp-EBW / 4-(5-{4-[DIMETHYL(PROP-2-ENYL)AMMONIO]PHENYL}-3-OXOPENTYL)-N,N-DIMETHYL-N-PROP-2-ENYLBENZENAMINIUM


Mass: 406.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H38N2O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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

Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 10 mM sodium citrate, 100 mM HEPES, pH 7, and 6-8 % PEG6000 or PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 66738 / % possible obs: 80.1 % / Redundancy: 1.2 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 14.5
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.642 / Num. unique obs: 8151

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.352→27.918 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.2447 3352 5.02 %
Rwork0.2038 --
obs0.2058 66738 70.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.352→27.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 88 217 8681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028725
X-RAY DIFFRACTIONf_angle_d0.60611927
X-RAY DIFFRACTIONf_dihedral_angle_d16.2035134
X-RAY DIFFRACTIONf_chiral_restr0.0431256
X-RAY DIFFRACTIONf_plane_restr0.0051575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.352-2.38560.4032190.3083505X-RAY DIFFRACTION13
2.3856-2.42110.3778440.3191862X-RAY DIFFRACTION23
2.4211-2.4590.3417610.30671505X-RAY DIFFRACTION39
2.459-2.49920.36991050.31842077X-RAY DIFFRACTION55
2.4992-2.54230.38791400.29932596X-RAY DIFFRACTION69
2.5423-2.58850.34451730.29542866X-RAY DIFFRACTION79
2.5885-2.63830.34711680.29543181X-RAY DIFFRACTION84
2.6383-2.69210.30641630.27963171X-RAY DIFFRACTION84
2.6921-2.75060.30861660.27013149X-RAY DIFFRACTION84
2.7506-2.81450.31171790.25763181X-RAY DIFFRACTION84
2.8145-2.88480.25441340.24113151X-RAY DIFFRACTION84
2.8848-2.96270.28251660.23853132X-RAY DIFFRACTION83
2.9627-3.04980.26761550.23213131X-RAY DIFFRACTION83
3.0498-3.14810.2791720.22753016X-RAY DIFFRACTION82
3.1481-3.26050.23211600.2133025X-RAY DIFFRACTION81
3.2605-3.39080.23711520.20593027X-RAY DIFFRACTION80
3.3908-3.54480.2171820.20382937X-RAY DIFFRACTION79
3.5448-3.73130.24241370.19442941X-RAY DIFFRACTION79
3.7313-3.96450.23611750.17862870X-RAY DIFFRACTION77
3.9645-4.26960.22451520.16492830X-RAY DIFFRACTION75
4.2696-4.69740.18611500.14642748X-RAY DIFFRACTION73
4.6974-5.37290.1921310.15252651X-RAY DIFFRACTION71
5.3729-6.75350.19661550.15892563X-RAY DIFFRACTION69
6.7535-27.91970.16521130.14212271X-RAY DIFFRACTION60

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