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

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Basic information

Entry
Database: PDB / ID: 1cfj
TitleMETHYLPHOSPHONYLATED ACETYLCHOLINESTERASE (AGED) OBTAINED BY REACTION WITH O-ISOPROPYLMETHYLPHOSPHONOFLUORIDATE (GB, SARIN)
ComponentsPROTEIN (ACETYLCHOLINESTERASE)
KeywordsHYDROLASE / CHOLINESTERASE / ORGANOPHOSPHATE / SERINE HYDROLASE / CHEMICAL-WARFARE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / 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 / Alpha/Beta hydrolase fold ...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
METHYLPHOSPHONIC ACID ESTER GROUP / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMillard, C.B. / Silman, I. / Sussman, J.L.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level.
Authors: Millard, C.B. / Kryger, G. / Ordentlich, A. / Greenblatt, H.M. / Harel, M. / Raves, M.L. / Segall, Y. / Barak, D. / Shafferman, A. / Silman, I. / Sussman, J.L.
#1: Journal: Structure and Function of Cholinesterases and Related Proteins
Year: 1998
Title: Crystal Structural of "Aged" Phosphorylated and Phosphonylated torpedo californica Acetylcholinesterase
Authors: Millard, C.B. / Kryger, G. / Ordentlich, A. / Harel, M. / Raves, M.L. / Greenblatt, H.M. / Segall, Y. / Barak, D. / Shafferman, A. / Silman, I. / Sussman, J.L.
History
DepositionMar 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 25, 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 9, 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: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2754
Polymers60,7371
Non-polymers5383
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.395, 111.395, 136.623
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
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 / N-Acetylglucosamine


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-GB / METHYLPHOSPHONIC ACID ESTER GROUP / Methylphosphonic acid


Mass: 96.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5O3P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
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, 4 DEG C , temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / 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 %(v/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: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 30011 / % possible obs: 97.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 40.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.17 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 200755 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.17

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Processing

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

2ace


Resolution: 2.6→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 3132443.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CONTINUOUS POSITIVE DIFFERENCE DENSITY IN (FO-FC) MAPS OCCURS IN FRONT OF THE INDOLE RINGS OF W84 AND W279. THIS DENSITY IS PRESENTLY MODELLED WITH WATERS 1007/1008/1009 (W84) AND WATERS 1003/1004/1005 (W279)
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1497 5.2 %RANDOM
Rwork0.186 ---
obs-28531 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.55 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.48 Å28.97 Å20 Å2
2--8.48 Å20 Å2
3----16.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 32 220 4496
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.271.5
X-RAY DIFFRACTIONx_mcangle_it3.42
X-RAY DIFFRACTIONx_scbond_it4.012
X-RAY DIFFRACTIONx_scangle_it5.342.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 288 5.9 %
Rwork0.224 4624 -
obs--98 %
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 DIFFRACTION4GB.PARGB.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 27034
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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