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- PDB-6ewk: T. californica AChE in complex with a 3-hydroxy-2-pyridine aldoxime. -

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Basic information

Entry
Database: PDB / ID: 6ewk
TitleT. californica AChE in complex with a 3-hydroxy-2-pyridine aldoxime.
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: 2.22 Å
Authorsde la Mora, E. / Weik, M. / Braiki, A. / Mougeot, R. / Jean, L. / Renard, P.I.
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
DepositionNov 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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)61,8668
Polymers60,1941
Non-polymers1,6727
Water7,332407
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,73216
Polymers120,3882
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.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 60193.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) 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: 299 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: Polyethylen glycol 200 36 % MES 100 mM pH 5.4

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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
ReflectionResolution: 2.22→29.12 Å / Num. obs: 48656 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 30.19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.062 / Rrim(I) all: 0.1239 / Net I/σ(I): 9.14
Reflection shellResolution: 2.22→2.299 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5683 / 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: 99.32

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→29.12 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.92
RfactorNum. reflection% reflection
Rfree0.2198 2014 4.14 %
Rwork0.1767 --
obs0.1785 48625 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.22→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 90 407 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014498
X-RAY DIFFRACTIONf_angle_d1.1856104
X-RAY DIFFRACTIONf_dihedral_angle_d16.791666
X-RAY DIFFRACTIONf_chiral_restr0.077639
X-RAY DIFFRACTIONf_plane_restr0.007790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.27550.2761440.26633330X-RAY DIFFRACTION99
2.2755-2.3370.28341430.25773279X-RAY DIFFRACTION99
2.337-2.40570.31411420.24093277X-RAY DIFFRACTION100
2.4057-2.48330.27081430.22693351X-RAY DIFFRACTION100
2.4833-2.5720.27761400.21143295X-RAY DIFFRACTION100
2.572-2.67490.27191360.20153294X-RAY DIFFRACTION100
2.6749-2.79660.26741430.193336X-RAY DIFFRACTION100
2.7966-2.94390.24331460.18523324X-RAY DIFFRACTION100
2.9439-3.12820.23951420.18233311X-RAY DIFFRACTION100
3.1282-3.36940.22411470.18183355X-RAY DIFFRACTION100
3.3694-3.70780.19141470.15343354X-RAY DIFFRACTION100
3.7078-4.24290.18251480.14183348X-RAY DIFFRACTION99
4.2429-5.34030.16341490.13533376X-RAY DIFFRACTION99
5.3403-29.12440.2011440.16813381X-RAY DIFFRACTION95

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