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- PDB-1vxo: METHYLPHOSPHONYLATED ACETYLCHOLINESTERASE (AGED) OBTAINED BY REAC... -

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Basic information

Entry
Database: PDB / ID: 1vxo
TitleMETHYLPHOSPHONYLATED ACETYLCHOLINESTERASE (AGED) 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 / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / 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 ...Acetylcholinesterase, fish/snake / : / 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
METHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMillard, C.B. / 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_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.auth_comp_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 / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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
Revision 2.2Oct 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

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Assembly

Deposited unit
A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2584
Polymers60,7371
Non-polymers5213
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.509, 112.509, 137.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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 (AGED)
Source: (natural) Torpedo californica (Pacific electric ray)
Cellular location: MEMBRANE BOUND BY GPI ANCHOR / Organ: ELECTRIC ORGAN / Tissue: ELECTROPLAQUE / References: UniProt: P04058, 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-VXA / METHYLPHOSPHONIC ACID ESTER GROUP


Mass: 79.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O2P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACHE WAS PHOSPHONYLATED WITH VX, THE CONJUGATE WAS CRYSTALLIZED, AND SUBSEQUENTLY ALLOWED TO ...ACHE WAS PHOSPHONYLATED WITH VX, THE CONJUGATE WAS CRYSTALLIZED, AND SUBSEQUENTLY ALLOWED TO UNDERGO COMPLETE AGING (DEALKYLATION OF THE OP ETHYL GROUP). THE STRUCTURE OF THE OP-ACHE CONJUGATE BEFORE AGING ALSO WAS SOLVED BY X-RAY DIFFRACTION, AND IS DEPOSITED UNDER A SEPARATE PDB ACCESSION CODE.
Has protein modificationY
Nonpolymer detailsANIONIC METHYLPHOSPHONATE ADDUCT COVALENTLY BOUND TO S200

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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: NSLS / Beamline: X12C / Wavelength: 0.98
DetectorType: BRANDEIS / Detector: CCD / Date: Mar 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 38823 / % possible obs: 97.2 % / Redundancy: 10.7 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.7
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.24 / % possible all: 80.5
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % possible obs: 97.2 %
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Mean I/σ(I) obs: 4

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Processing

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

2ace


Resolution: 2.4→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1956322.52 / 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 1074/1075/1077 (W84) AND WATERS 1079/1087/1127/1107 (W279).
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1923 5 %RANDOM
Rwork0.194 ---
obs0.194 38787 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.82 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.26 Å24.46 Å20 Å2
2--7.26 Å20 Å2
3----14.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 32 216 4492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg2.1
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_d1.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 286 5.2 %
Rwork0.238 5213 -
obs--83.7 %
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 DIFFRACTION4VXA.PARVXA.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å
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_deg1.38
X-RAY DIFFRACTIONc_mcbond_it1.08
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_mcangle_it1.75
X-RAY DIFFRACTIONc_scangle_it2.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.238

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