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- PDB-6o52: Room temperature structure of binary complex of native hAChE with... -

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Basic information

Entry
Database: PDB / ID: 6o52
TitleRoom temperature structure of binary complex of native hAChE with BW284c51
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / BW284c51
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / retina development in camera-type eye / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleus / membrane / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
Chem-EBW / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3894
Polymers120,5762
Non-polymers8132
Water54030
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3894
Polymers120,5762
Non-polymers8132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
Buried area3990 Å2
ΔGint-10 kcal/mol
Surface area39050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.434, 125.434, 130.592
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.99 Å3/Da / Density % sol: 75.34 %
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 29380 / % possible obs: 81.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.1
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.504 / Num. unique obs: 3263

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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: 3.2→39.168 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.01
RfactorNum. reflection% reflection
Rfree0.1888 1421 4.84 %
Rwork0.1531 --
obs0.1549 29380 77.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→39.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 60 30 8466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038702
X-RAY DIFFRACTIONf_angle_d0.55111904
X-RAY DIFFRACTIONf_dihedral_angle_d14.635126
X-RAY DIFFRACTIONf_chiral_restr0.0411256
X-RAY DIFFRACTIONf_plane_restr0.0051574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1996-3.31390.29791540.2332572X-RAY DIFFRACTION72
3.3139-3.44650.27911410.22752765X-RAY DIFFRACTION77
3.4465-3.60330.2041480.1912859X-RAY DIFFRACTION79
3.6033-3.79310.23471440.17542901X-RAY DIFFRACTION81
3.7931-4.03050.19841480.1592989X-RAY DIFFRACTION82
4.0305-4.34140.21261280.14552967X-RAY DIFFRACTION82
4.3414-4.77760.14391350.12432920X-RAY DIFFRACTION81
4.7776-5.46730.15881500.13882843X-RAY DIFFRACTION78
5.4673-6.88220.19121260.14632727X-RAY DIFFRACTION76
6.8822-39.17060.14071470.12082416X-RAY DIFFRACTION68

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