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- PDB-1vxr: O-ETHYLMETHYLPHOSPHONYLATED ACETYLCHOLINESTERASE OBTAINED BY REAC... -

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Basic information

Entry
Database: PDB / ID: 1vxr
TitleO-ETHYLMETHYLPHOSPHONYLATED ACETYLCHOLINESTERASE OBTAINED BY REACTION WITH O-ETHYL-S-[2-[BIS(1-METHYLETHYL)AMINO]ETHYL] METHYLPHOSPHONOTHIOATE (VX)
ComponentsPROTEIN (ACETYLCHOLINESTERASE)
KeywordsHYDROLASE / CHOLINESTERASE / ORGANOPHOSPHATE / SERINE HYDROLASE / CHEMICAL-WARFARE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / 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, fish/snake / : / 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
O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMillard, C.B. / Koellner, G. / Silman, I. / Sussman, J.L.
CitationJournal: J.Am.Chem.Soc. / Year: 1999
Title: Reaction Products of Acetylcholinesterase and VX Reveal a Mobile Histidine in the Catalytic Triad
Authors: Millard, C.B. / Koellner, G. / Ordentlich, A. / Shafferman, A. / Silman, I. / Sussman, J.L.
History
DepositionApr 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 15, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 2, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_assembly.oligomeric_count ..._chem_comp.pdbx_synonyms / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 2.2Aug 23, 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 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8976
Polymers60,7371
Non-polymers1,1605
Water6,107339
1
A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules

A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,79312
Polymers121,4732
Non-polymers2,32010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)112.836, 112.836, 137.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (ACETYLCHOLINESTERASE)


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPLEXED WITH THE NERVE AGENT VX
Source: (natural) Torpedo californica (Pacific electric ray)
Cellular location: MEMBRANE BOUND BY GPI ANCHOR / Organ: ELECTRIC ORGAN / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 1
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 , 3 types, 342 molecules

#4: Chemical ChemComp-VX / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP


Mass: 124.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O3P
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsACHE WAS PHOSPHONYLATED WITH VX, THE CONJUGATE WAS CRYSTALLIZED, AND THE NON-AGED STRUCTURE WAS ...ACHE WAS PHOSPHONYLATED WITH VX, THE CONJUGATE WAS CRYSTALLIZED, AND THE NON-AGED STRUCTURE WAS SOLVED. THE AGED CONJUGATE (COMPLETE DEALKYLATION OF OP ETHYL GROUP) ALSO WAS SOLVED BY X-RAY DIFFRACTION, AND IS DEPOSITED UNDER A SEPARATE PDB ACCESSION CODE.
Has protein modificationY
Nonpolymer detailsO-ETHYLMETHYLPHOSPHONATE ADDUCT COVALENTLY BOUND TO S200 TWO MES MOLECULES (CRYSTALLIZATION BUFFER) ...O-ETHYLMETHYLPHOSPHONATE ADDUCT COVALENTLY BOUND TO S200 TWO MES MOLECULES (CRYSTALLIZATION BUFFER) ARE INCLUDED IN THE PRESENT MODEL.

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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: 3.8 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / pH: 6
Details: 35-40% (W/V) PEG-200 0.15 M MES BUFFER PH 6, 0.05 M NACL, pH 6.00, temperature 277.00K
Crystal
*PLUS
Density % sol: 68 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Millard, C.B., (1999) Biochemistry, 38, 7032. / PH range low: 6 / PH range high: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
235-40 %(w/v)PEG2001reservoir
30.15 MMES1reservoir
40.05 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.002
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 47840 / % possible obs: 92.3 % / Redundancy: 8.2 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.32 / % possible all: 83.9
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 92.3 % / Redundancy: 8.2 %
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Mean I/σ(I) obs: 1.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACE

2ace


Resolution: 2.2→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2738492.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: USED COMPOSITE-OMIT MAP METHOD CONTINUOUS POSITIVE DIFFERENCE DENSITY IN (FO-FC) MAPS OCCURS IN FRONT OF THE INDOLE RINGS OF W84 AND W279. THIS DENSITY IS PRESENTLY MODELED WITH WATERS ...Details: USED COMPOSITE-OMIT MAP METHOD CONTINUOUS POSITIVE DIFFERENCE DENSITY IN (FO-FC) MAPS OCCURS IN FRONT OF THE INDOLE RINGS OF W84 AND W279. THIS DENSITY IS PRESENTLY MODELED WITH WATERS 1007/1008/1009 (W84) AND WATERS 1005/1003/1004/1002 (W279)
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2154 5 %RANDOM
Rwork0.189 ---
obs-43083 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.36 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-7 Å24.75 Å20 Å2
2--7 Å20 Å2
3----13.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 72 339 4655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.611.5
X-RAY DIFFRACTIONc_mcangle_it1.082
X-RAY DIFFRACTIONc_scbond_it0.932
X-RAY DIFFRACTIONc_scangle_it1.482.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 167 4.4 %
Rwork0.274 3644 -
obs--44.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4VX.PARVX.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Rfactor obs: 0.189 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32
X-RAY DIFFRACTIONc_mcbond_it0.61
X-RAY DIFFRACTIONc_scbond_it0.93
X-RAY DIFFRACTIONc_mcangle_it1.08
X-RAY DIFFRACTIONc_scangle_it1.48
LS refinement shell
*PLUS
Rfactor Rfree: 0.266 / Rfactor Rwork: 0.274

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