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- PDB-6g17: Non-aged form of Torpedo californica acetylcholinesterase inhibit... -

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Basic information

Entry
Database: PDB / ID: 6g17
TitleNon-aged form of Torpedo californica acetylcholinesterase inhibited by nerve agent tabun
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / tabun / nerve agent
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
R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSantoni, G. / De la Mora, E. / de Souza, J. / Silman, I. / Sussman, J. / Baati, R. / Weik, M. / Nachon, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyReAChE France
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents.
Authors: Santoni, G. / de Sousa, J. / de la Mora, E. / Dias, J. / Jean, L. / Sussman, J.L. / Silman, I. / Renard, P.Y. / Brown, R.C.D. / Weik, M. / Baati, R. / Nachon, F.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,18313
Polymers60,7371
Non-polymers1,44712
Water8,035446
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,36626
Polymers121,4732
Non-polymers2,89324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area7060 Å2
ΔGint50 kcal/mol
Surface area38810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.767, 111.767, 137.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-705-

HOH

21A-1053-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Acetylcholinesterase / / AChE


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetronarce californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#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 / 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

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Non-polymers , 5 types, 456 molecules

#2: Chemical ChemComp-NTJ / R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE


Mass: 137.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO2P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 150mM MES pH 5.6 36% PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.74 Å / Num. all: 50213 / Num. obs: 274775 / % possible obs: 98.84 % / Redundancy: 5.5 % / Rrim(I) all: 0.08 / Net I/σ(I): 13.67
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.5 % / Num. unique obs: 27951 / % possible all: 98.55

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ea5

1ea5


Resolution: 2.2→45.738 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2138 1507 3 %
Rwork0.173 --
obs0.1742 50208 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 93 449 4786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084532
X-RAY DIFFRACTIONf_angle_d0.916147
X-RAY DIFFRACTIONf_dihedral_angle_d16.1892681
X-RAY DIFFRACTIONf_chiral_restr0.054641
X-RAY DIFFRACTIONf_plane_restr0.005796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27110.34091340.32624336X-RAY DIFFRACTION98
2.2711-2.35220.28171360.28874394X-RAY DIFFRACTION99
2.3522-2.44640.33411370.26724413X-RAY DIFFRACTION99
2.4464-2.55770.30231350.24524387X-RAY DIFFRACTION100
2.5577-2.69260.28961380.22224449X-RAY DIFFRACTION100
2.6926-2.86120.2751370.19354445X-RAY DIFFRACTION100
2.8612-3.08210.2111380.17564433X-RAY DIFFRACTION100
3.0821-3.39220.20341380.15354465X-RAY DIFFRACTION100
3.3922-3.88280.17921370.13064433X-RAY DIFFRACTION99
3.8828-4.89110.15121380.12274456X-RAY DIFFRACTION98
4.8911-45.74820.20121390.16854490X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -51.1153 Å / Origin y: 31.9887 Å / Origin z: -33.4365 Å
111213212223313233
T0.2654 Å2-0.0002 Å20.0147 Å2-0.2137 Å2-0.0164 Å2--0.2626 Å2
L1.3035 °20.1789 °2-0.4569 °2-1.0112 °2-0.0585 °2--1.9671 °2
S0.0221 Å °0.0112 Å °-0.1053 Å °0.0194 Å °-0.0547 Å °-0.0134 Å °0.1519 Å °-0.0224 Å °0.0366 Å °
Refinement TLS groupSelection details: chain 'A'

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