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- PDB-6fqn: Carbamylated T. californica acetylcholineterase bound to uncharge... -

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Basic information

Entry
Database: PDB / ID: 6fqn
TitleCarbamylated T. californica acetylcholineterase bound to uncharged hybrid reactivator 2
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Acetylcholinesterase Hybrid reactivators Organophosphate inhibition Structure-based optimization
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-E2W / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.30002662121 Å
AuthorsDe la Mora, E. / Santoni, G. / de Souza, J. / Sussman, J. / Silman, I. / Baati, R. / Weik, M. / Nachon, F.
Funding support France, 2items
OrganizationGrant numberCountry
French Ministry of Armed Forces (DGA and SSA) France
ANR ASTRID programReCNSAChE 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
DepositionFeb 14, 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

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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)61,98914
Polymers60,2791
Non-polymers1,71013
Water2,936163
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,97828
Polymers120,5582
Non-polymers3,41926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6770 Å2
ΔGint-90 kcal/mol
Surface area39490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.430, 113.430, 137.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein Acetylcholinesterase / / AChE


Mass: 60279.078 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
#3: 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

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-E2W / 6-[4-[(7-chloranyl-1,2,3,4-tetrahydroacridin-9-yl)amino]butyl]-2-[(oxidanylamino)methyl]pyridin-3-ol


Mass: 426.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 4.24 Å3/Da / Density % sol: 70.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: MES 100 mM pH 5.4 PEG 200 28%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→39.98 Å / Num. obs: 45946 / % possible obs: 99.72 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 41.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.042 / Rrim(I) all: 0.115 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4513 / CC1/2: 0.812 / Rpim(I) all: 0.285 / Rrim(I) all: 0.7493 / % possible all: 99.73

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.30002662121→39.9721095433 Å / SU ML: 0.336235589523 / Cross valid method: FREE R-VALUE / σ(F): 1.35120167119 / Phase error: 28.7743616241
RfactorNum. reflection% reflection
Rfree0.234082470929 2000 4.36233559448 %
Rwork0.20514979002 --
obs0.206455335956 45847 99.7519636213 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.7376603806 Å2
Refinement stepCycle: LAST / Resolution: 2.30002662121→39.9721095433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4250 0 105 163 4518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007028582456164503
X-RAY DIFFRACTIONf_angle_d1.031631559436114
X-RAY DIFFRACTIONf_chiral_restr0.0570629963765638
X-RAY DIFFRACTIONf_plane_restr0.00685387640284791
X-RAY DIFFRACTIONf_dihedral_angle_d23.60445756411654

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