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- PDB-1som: TORPEDO CALIFORNICA ACETYLCHOLINESTERASE INHIBITED BY NERVE AGENT... -

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Basic information

Entry
Database: PDB / ID: 1som
TitleTORPEDO CALIFORNICA ACETYLCHOLINESTERASE INHIBITED BY NERVE AGENT GD (SOMAN).
ComponentsPROTEIN (ACETYLCHOLINESTERASE)
KeywordsSERINE HYDROLASE / CHOLINESTERASE / NERVE AGENT / ORGANOPHOSPHOROUS ACID ANHYDRIDE
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 / OTHER / Resolution: 2.2 Å
AuthorsGreenblatt, H.M. / Millard, C.B. / Sussman, J.L. / Silman, I.
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. / Greenblat, H.M. / Segall, Y. / Barak, D. / Shafferman, A. / Silman, I. / Sussman, J.L.
History
DepositionMar 17, 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 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jun 2, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_assembly.details ..._chem_comp.pdbx_synonyms / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _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)61,84714
Polymers61,3251
Non-polymers52113
Water3,315184
1
A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules

A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,69328
Polymers122,6502
Non-polymers1,04326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3080 Å2
ΔGint2 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.560, 111.560, 137.002
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: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: NERVE AGENT GD (SOMAN) COVALENTLY BOUND TO CATALYTIC SERINE (SER200)
Source: (natural) Torpedo californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / 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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#4: Chemical ChemComp-VXA / METHYLPHOSPHONIC ACID ESTER GROUP / Methylphosphinic acid


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


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGD (SOMAN) HAS UNDERGONE DEALKYLATION AND THE PINACOLYL GROUP IS NOT VISIBLE IN THE ELECTRON ...GD (SOMAN) HAS UNDERGONE DEALKYLATION AND THE PINACOLYL GROUP IS NOT VISIBLE IN THE ELECTRON DENSITY MAPS. DUMMY ATOMS NOT USED IN REFINEMENT TO SHOW LOCATION OF TWO DENSITY FEATURES NEAR THE INDOLE RINGS OF TRP84 AND TRP279

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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: PROTEIN WAS CRYSTALLIZED FROM 35-40% W/V PEG 200 0.15M MES PH 6.0 0.05M NACL 4 DEG. CELSIUS , 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 %(w/v)PEG2001reservoir
30.15 MMES1reservoir
40.05 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 49048 / % possible obs: 96.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.297 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 286328 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.3

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Processing

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

2ace


Resolution: 2.2→29.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2163305.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINED INITIALLY WITH REFMAC TO AN R OF 23.4 AND RFREE OF 27.9 CONTINUOUS ELECTRON DENSITY FEATURES IN FRONT OF THE INDOLE RINGS OF TRP84 AND TRP279 DID NOT SATISFACTORILY REFINE WITH WATER ...Details: REFINED INITIALLY WITH REFMAC TO AN R OF 23.4 AND RFREE OF 27.9 CONTINUOUS ELECTRON DENSITY FEATURES IN FRONT OF THE INDOLE RINGS OF TRP84 AND TRP279 DID NOT SATISFACTORILY REFINE WITH WATER MOLECULES. THESE FEATURES WERE LEFT EMPTY DURING REFINEMENT, BUT THEIR POSITIONS ARE INDICATED IN THE MODEL BY OXYGEN ATOMS WITH ZERO OCCUPANCY (RESIDUES 1000 - 1009)
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2460 5 %RANDOM
Rwork0.21 ---
obs-48792 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.78 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.77 Å23.42 Å20 Å2
2--7.77 Å20 Å2
3----15.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 42 184 4400
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 398 5.1 %
Rwork0.264 7455 -
obs--94.5 %
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 DIFFRACTION4CIS_PEPTIDE.PARAMSOMAN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
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_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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