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- PDB-2y2v: Nonaged form of Mouse Acetylcholinesterase inhibited by sarin-Update -

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Basic information

Entry
Database: PDB / ID: 2y2v
TitleNonaged form of Mouse Acetylcholinesterase inhibited by sarin-Update
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / CHOLINESTERASE / METHYLPHOSPHONATE
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis ...acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / laminin binding / side of membrane / synapse assembly / collagen binding / neuromuscular junction / response to insulin / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / hydrolase activity / cell adhesion / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / 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-ETHOXYETHANOL / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAkfur, C. / Artursson, E. / Ekstrom, F.
CitationJournal: To be Published
Title: Methylphosphonate Adducts of Acetylcholinesterase Investigated by Time Correlated Single Photon Counting and X-Ray Crystallography
Authors: Akfur, C. / Artursson, E. / Ekstrom, F.
History
DepositionDec 16, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionNov 30, 2011ID: 2JGG
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Other
Revision 1.2Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)122,37312
Polymers120,7082
Non-polymers1,66510
Water13,097727
1
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5598
Polymers60,3541
Non-polymers1,2057
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8144
Polymers60,3541
Non-polymers4603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.488, 111.643, 227.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.735238, -0.403452, -0.545658), (-0.405135, -0.905799, 0.12407), (-0.543407, 0.129439, -0.82943)
Vector: 1.07587, 23.9332, -13.3859)

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 60354.070 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293F / 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.: 3
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 , 5 types, 734 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ME2 / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 148.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O3
#5: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#6: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsRESIDUE SGB REPRESENTS CATALYTIC SER 203 PHOSPHONYLATED BY SARIN.

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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: 3.9 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 7 / Details: 26-30% (V/V) PEG 750MME, 0.1 M HEPES PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: May 13, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 2.45→29.14 Å / Num. obs: 306983 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 50.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.45→28.979 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1474 2 %
Rwork0.1847 --
obs0.1854 74170 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.816 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6269 Å20 Å20 Å2
2--2.1234 Å20 Å2
3----3.7503 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 109 727 9108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078704
X-RAY DIFFRACTIONf_angle_d1.11911870
X-RAY DIFFRACTIONf_dihedral_angle_d18.0563124
X-RAY DIFFRACTIONf_chiral_restr0.0751276
X-RAY DIFFRACTIONf_plane_restr0.0051550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5290.2681260.2426539X-RAY DIFFRACTION99
2.529-2.61940.28811260.22626520X-RAY DIFFRACTION99
2.6194-2.72420.26561510.22296588X-RAY DIFFRACTION99
2.7242-2.8480.28641340.21326599X-RAY DIFFRACTION100
2.848-2.99810.26741330.21956566X-RAY DIFFRACTION100
2.9981-3.18570.25531530.20726646X-RAY DIFFRACTION100
3.1857-3.43130.22351140.18876630X-RAY DIFFRACTION100
3.4313-3.77590.20061450.16416611X-RAY DIFFRACTION99
3.7759-4.32080.18471250.14726621X-RAY DIFFRACTION99
4.3208-5.43780.1661310.13576651X-RAY DIFFRACTION98
5.4378-28.98110.20331360.16926725X-RAY DIFFRACTION96

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