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- PDB-6euc: Reactivating oxime bound to Tc AChE's catalytic gorge. -

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Basic information

Entry
Database: PDB / ID: 6euc
TitleReactivating oxime bound to Tc AChE's catalytic gorge.
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Acetylcholinesterase / reactivator / aldehyde oxime / organophosphate poisoning
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
Chem-RM0 / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21998854547 Å
Authorsde la Mora, E. / Weik, M. / Braiki, A. / Mougeot, R. / Jean, L. / Renard, P.I.
Funding support France, 1items
OrganizationGrant numberCountry
Commissariat ? l'Energie Atomique et aux Energies AlternativesNRBC France
CitationJournal: Chemistry / Year: 2018
Title: Potent 3-Hydroxy-2-Pyridine Aldoxime Reactivators of Organophosphate-Inhibited Cholinesterases with Predicted Blood-Brain Barrier Penetration.
Authors: Zorbaz, T. / Braiki, A. / Marakovic, N. / Renou, J. / de la Mora, E. / Macek Hrvat, N. / Katalinic, M. / Silman, I. / Sussman, J.L. / Mercey, G. / Gomez, C. / Mougeot, R. / Perez, B. / ...Authors: Zorbaz, T. / Braiki, A. / Marakovic, N. / Renou, J. / de la Mora, E. / Macek Hrvat, N. / Katalinic, M. / Silman, I. / Sussman, J.L. / Mercey, G. / Gomez, C. / Mougeot, R. / Perez, B. / Baati, R. / Nachon, F. / Weik, M. / Jean, L. / Kovarik, Z. / Renard, P.Y.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9878
Polymers65,3161
Non-polymers1,6727
Water7,332407
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,97516
Polymers130,6312
Non-polymers3,34414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_797x-y+2,-y+4,-z+8/31
Unit cell
Length a, b, c (Å)111.520, 111.520, 136.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 65315.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetronarce californica (Pacific electric ray)
Gene: ache
Production host: Tetronarce californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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-RM0 / 2-[(~{E})-hydroxyiminomethyl]-6-(5-morpholin-4-ylpentyl)pyridin-3-ol


Mass: 293.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: MES 100 mM p H 5.4. PEG 200 36 %.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 29.9989723284 Å2
Reflection shellResolution: 2.22→2.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5684 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4819 / CC1/2: 0.772 / Rpim(I) all: 0.3366 / Rrim(I) all: 0.6652 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21998854547→29.1218974687 Å / SU ML: 0.243071086826 / Cross valid method: FREE R-VALUE / σ(F): 1.34360509285 / Phase error: 22.9173146747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219823723266 2014 4.14190231362 %
Rwork0.176675605137 46611 -
obs0.178456516611 48625 99.1638625472 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.4443697772 Å2
Refinement stepCycle: LAST / Resolution: 2.21998854547→29.1218974687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 90 407 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01019721956544498
X-RAY DIFFRACTIONf_angle_d1.184781752066104
X-RAY DIFFRACTIONf_chiral_restr0.077410823596639
X-RAY DIFFRACTIONf_plane_restr0.0067743096609790
X-RAY DIFFRACTIONf_dihedral_angle_d16.78988813161666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.27550.2759868110861440.266316007813330X-RAY DIFFRACTION99.3422933943
2.2755-2.3370.2833511279211430.2577406555433279X-RAY DIFFRACTION99.4478349317
2.337-2.40570.3140985832861420.2409177442323277X-RAY DIFFRACTION99.5631916133
2.4057-2.48330.2707548736241430.2269200145843351X-RAY DIFFRACTION99.5158074623
2.4833-2.5720.2775845879981400.2114191941783295X-RAY DIFFRACTION99.8256320837
2.572-2.67490.2719319722811360.2014707892123294X-RAY DIFFRACTION99.8253783469
2.6749-2.79660.2673838713751430.1900412262643336X-RAY DIFFRACTION99.5137299771
2.7966-2.94390.2432958961121460.1852249161043324X-RAY DIFFRACTION99.598163031
2.9439-3.12820.2394924843511420.1823131844243311X-RAY DIFFRACTION99.5961926738
3.1282-3.36940.224071472151470.1817579893393355X-RAY DIFFRACTION99.715261959
3.3694-3.70780.1913535547791470.1534243008583354X-RAY DIFFRACTION99.6300512237
3.7078-4.24290.182513693241480.1417513142753348X-RAY DIFFRACTION99.1210660618
4.2429-5.34030.1633784548931490.1352967114083376X-RAY DIFFRACTION98.6289871293
5.3403-29.12440.201032542281440.1680597699943381X-RAY DIFFRACTION95.2445285058

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