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

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Basic information

Entry
Database: PDB / ID: 2whp
TitleCrystal structure of acetylcholinesterase, phosphonylated by sarin and in complex with HI-6
Components(ACETYLCHOLINESTERASE) x 2
KeywordsHYDROLASE / SERINE ESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / HI-6 / SARIN / SYNAPSE / MEMBRANE / SECRETED / CELL MEMBRANE / DISULFIDE BOND / CHOLINESTERASE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / collagen binding / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / 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
CARBONATE ION / Chem-HI6 / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.5Dec 13, 2023Group: Data collection / Database references ...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
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)122,38410
Polymers120,6952
Non-polymers1,6898
Water14,286793
1
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1455
Polymers60,3541
Non-polymers7914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2395
Polymers60,3411
Non-polymers8984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.260, 112.150, 226.950
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 , 2 types, 2 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60354.070 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-573
Source method: isolated from a genetically manipulated source
Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN / 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: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60341.031 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-573
Source method: isolated from a genetically manipulated source
Details: CATALYTIC SER203 PHOSPHONYLATED BY SARIN / 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

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Sugars , 1 types, 3 molecules

#3: 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


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, 798 molecules

#4: 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
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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→29.8 Å / Num. obs: 102346 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 38.88 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.1 / % possible all: 98.9

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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

1j06


Resolution: 2.2→28.988 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 20.21 / Stereochemistry target values: ML / Details: RESIDUES 258-264 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.21 2048 2 %
Rwork0.1754 --
obs0.1761 102274 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.363 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9857 Å2-0 Å20 Å2
2---0.8695 Å20 Å2
3---3.8553 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8275 0 104 793 9172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138699
X-RAY DIFFRACTIONf_angle_d1.42511877
X-RAY DIFFRACTIONf_dihedral_angle_d18.9573103
X-RAY DIFFRACTIONf_chiral_restr0.0911276
X-RAY DIFFRACTIONf_plane_restr0.0071559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.31491620.29646542X-RAY DIFFRACTION99
2.2512-2.30740.29081270.25866570X-RAY DIFFRACTION99
2.3074-2.36980.2691370.24036601X-RAY DIFFRACTION99
2.3698-2.43950.27411280.22866589X-RAY DIFFRACTION99
2.4395-2.51820.23491170.20236616X-RAY DIFFRACTION99
2.5182-2.60810.2171380.17856651X-RAY DIFFRACTION99
2.6081-2.71250.23311540.17126615X-RAY DIFFRACTION99
2.7125-2.83580.21951340.16826658X-RAY DIFFRACTION99
2.8358-2.98520.20531330.15826682X-RAY DIFFRACTION99
2.9852-3.1720.17761490.16236681X-RAY DIFFRACTION99
3.172-3.41660.20161170.15926715X-RAY DIFFRACTION99
3.4166-3.75980.18591450.14636748X-RAY DIFFRACTION99
3.7598-4.30230.15941350.13376758X-RAY DIFFRACTION99
4.3023-5.41470.16371340.13066855X-RAY DIFFRACTION100
5.4147-28.99070.21371380.18646945X-RAY DIFFRACTION97
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)
10.4396-0.09380.17210.4712-0.1491.3064-0.03660.026800.02680.0218-0.01740.0992-0.05580.00970.0942-0.0058-0.00470.08670.02460.121627.31512.480216.5628
20.3902-0.06640.28020.66540.44841.76430.10630.0459-0.02940.0655-0.0680.05760.1588-0.0106-0.02890.162-0.0078-0.03490.1676-0.0470.17567.61184.697-40.3581
30.1118-0.03990.18590.09830.03160.4020.00270.0121-0.04320.0067-0.00660.0010.04810.0191-0.00750.0925-0.00220.00960.099-0.00070.108221.02859.3524-6.8962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN W

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