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- PDB-2whq: Crystal structure of acetylcholinesterase, phosphonylated by sari... -

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Basic information

Entry
Database: PDB / ID: 2whq
TitleCrystal structure of acetylcholinesterase, phosphonylated by sarin (aged) in complex with HI-6
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / HI-6 / SYNAPSE / MEMBRANE / SECRETED / NEUROTRANSMITTER DEGRADATION / CHOLINESTERASE / SERINE ESTERASE / ALTERNATIVE SPLICING / CELL JUNCTION / CELL MEMBRANE / DISULFIDE BOND / AGED SARIN / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN
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
Chem-HI6 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEkstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.G. / Schneider, G. / Pang, Y.P.
CitationJournal: Plos One / Year: 2009
Title: Structure of Hi-6Sarin-Acetylcholinesterase Determined by X-Ray Crystallography and Molecular Dynamics Simulation: Reactivator Mechanism and Design.
Authors: Ekstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.G. / Schneider, G. / Pang, Y.P.
History
DepositionMay 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 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 1.5May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 1.6Dec 13, 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

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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)122,85313
Polymers120,6242
Non-polymers2,22911
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint35 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.550, 112.320, 227.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 60311.992 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. THE COMPLEX WAS SUBSEQUENTLY AGED
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1
Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
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, 658 molecules

#3: Chemical ChemComp-HI6 / 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM / 1-(2-HYDROXY-IMINOMETHYLPYRIDINIUM)-1-(4-CARBOXYAMINO)-PYRIDINIUM DIMETHYLETHER


Mass: 288.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7 / Details: 26-30 % (V/V) PEG750MME 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.041
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.2→29.2 Å / Num. obs: 110895 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 45.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9

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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
Resolution: 2.15→29.089 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 20.38 / Stereochemistry target values: ML / Details: RESIDUES 258-264 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2119 2191 2 %
Rwork0.1855 --
obs0.186 110749 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.001 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8764 Å20 Å20 Å2
2--0.7953 Å20 Å2
3---0.0811 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8313 0 132 650 9095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018737
X-RAY DIFFRACTIONf_angle_d1.23511909
X-RAY DIFFRACTIONf_dihedral_angle_d18.2373130
X-RAY DIFFRACTIONf_chiral_restr0.0851280
X-RAY DIFFRACTIONf_plane_restr0.0061562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.19670.37141230.35236658X-RAY DIFFRACTION99
2.1967-2.24780.27621410.26866743X-RAY DIFFRACTION100
2.2478-2.3040.27111390.22686691X-RAY DIFFRACTION100
2.304-2.36630.26681470.21236720X-RAY DIFFRACTION100
2.3663-2.43590.2351310.20756776X-RAY DIFFRACTION100
2.4359-2.51450.21321150.1836754X-RAY DIFFRACTION100
2.5145-2.60430.21021470.17786766X-RAY DIFFRACTION100
2.6043-2.70850.22571510.16986741X-RAY DIFFRACTION100
2.7085-2.83160.20791330.17426784X-RAY DIFFRACTION100
2.8316-2.98080.20641370.1716796X-RAY DIFFRACTION100
2.9808-3.16730.18911480.17696785X-RAY DIFFRACTION100
3.1673-3.41150.20721250.17366831X-RAY DIFFRACTION100
3.4115-3.75420.16631460.1586839X-RAY DIFFRACTION100
3.7542-4.2960.17391340.14026880X-RAY DIFFRACTION100
4.296-5.40680.15311370.13496938X-RAY DIFFRACTION100
5.4068-29.09210.19641370.18126856X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6099-0.12010.08940.5173-0.23021.4607-0.03790.0316-0.00270.02090.01890.00220.1179-0.07150.01830.2717-0.00710.00320.25130.01820.275227.072912.30216.6363
20.5673-0.01110.33310.79570.41331.99250.10260.061-0.0450.0504-0.070.06690.19430.0211-0.02650.2751-0.0115-0.03250.2859-0.05040.28157.52174.9684-40.2912
30.151-0.07210.14240.0325-0.04570.36220.01350.0206-0.0581-0.0086-0.0096-0.00720.09790.0485-0.00450.2948-0.01630.00170.2910.00040.284921.38659.2199-8.1312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN W

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