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- PDB-4bc0: Structure of mouse acetylcholinesterase inhibited by CBDP (12-h s... -

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Basic information

Entry
Database: PDB / ID: 4bc0
TitleStructure of mouse acetylcholinesterase inhibited by CBDP (12-h soak) : Cresyl-phosphoserine adduct
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / BUTYRYLCHOLINESTERASE / NERVE TRANSMISSION / INHIBITION / ALPHA-BETA HYDROLASE
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / laminin binding / side of membrane / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
(2-methylphenyl) dihydrogen phosphate / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsCarletti, E. / Colletier, J.-P. / Schopfer, L.M. / Santoni, G. / Masson, P. / Lockridge, O. / Nachon, F. / Weik, M.
CitationJournal: Chem.Res.Toxicol. / Year: 2013
Title: Inhibition Pathways of the Potent Organophosphate Cbdp with Cholinesterases Revealed by X-Ray Crystallographic Snapshots and Mass Spectrometry
Authors: Carletti, E. / Colletier, J.-P. / Schopfer, L.M. / Santoni, G. / Masson, P. / Lockridge, O. / Nachon, F. / Weik, M.
History
DepositionSep 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _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_asym_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: 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
B: ACETYLCHOLINESTERASE
C: ACETYLCHOLINESTERASE
D: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,89136
Polymers239,0584
Non-polymers3,83332
Water7,404411
1
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,33715
Polymers119,5292
Non-polymers1,80813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-106.5 kcal/mol
Surface area38450 Å2
MethodPISA
2
C: ACETYLCHOLINESTERASE
D: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,55421
Polymers119,5292
Non-polymers2,02519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-124.6 kcal/mol
Surface area39140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.940, 174.040, 225.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 203 OR RESSEQ 600)
211CHAIN B AND (RESSEQ 203 OR RESSEQ 600)
311CHAIN C AND (RESSEQ 203 OR RESSEQ 600)
411CHAIN D AND (RESSEQ 203 OR RESSEQ 600)

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Components

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Protein / Sugars , 2 types, 11 molecules ABCD

#1: Protein
ACETYLCHOLINESTERASE


Mass: 59764.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CRESYL-PHOSPHATE ADDUCT ON S203 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P21836, 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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 , 4 types, 436 molecules

#2: Chemical
ChemComp-4OJ / (2-methylphenyl) dihydrogen phosphate / o-cresyl-phosphate


Mass: 188.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9O4P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 5.63 Å3/Da / Density % sol: 78 % / Description: NONE
Crystal growpH: 7.4
Details: 0.1 M TRIS HCL BUFFER PH 7.4, 1.6 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3.35→48.6 Å / Num. obs: 75488 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 3.35→3.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A16

4a16


Resolution: 3.35→48.615 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 2265 3 %
Rwork0.1618 --
obs0.1631 75467 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→48.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16806 0 215 411 17432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917527
X-RAY DIFFRACTIONf_angle_d1.48223960
X-RAY DIFFRACTIONf_dihedral_angle_d17.1366287
X-RAY DIFFRACTIONf_chiral_restr0.1082568
X-RAY DIFFRACTIONf_plane_restr0.0083140
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A17X-RAY DIFFRACTIONPOSITIONAL
12B17X-RAY DIFFRACTIONPOSITIONAL0.033
13C17X-RAY DIFFRACTIONPOSITIONAL0.042
14D17X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.42280.33241410.30994577X-RAY DIFFRACTION98
3.4228-3.50240.33061420.27244587X-RAY DIFFRACTION98
3.5024-3.590.32311430.24344602X-RAY DIFFRACTION98
3.59-3.6870.28781420.22014591X-RAY DIFFRACTION98
3.687-3.79550.22941410.19674575X-RAY DIFFRACTION98
3.7955-3.91790.23411420.17964575X-RAY DIFFRACTION98
3.9179-4.05790.21541420.15884611X-RAY DIFFRACTION98
4.0579-4.22030.18011410.14784556X-RAY DIFFRACTION98
4.2203-4.41220.16611430.13114605X-RAY DIFFRACTION97
4.4122-4.64470.16391400.11884553X-RAY DIFFRACTION97
4.6447-4.93540.17081420.11464565X-RAY DIFFRACTION96
4.9354-5.31610.15121410.11994555X-RAY DIFFRACTION96
5.3161-5.85020.18451410.12844574X-RAY DIFFRACTION96
5.8502-6.69490.21211410.14814547X-RAY DIFFRACTION95
6.6949-8.42770.20131400.15254523X-RAY DIFFRACTION94
8.4277-48.61980.19971430.17254606X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9249-0.1518-0.1281.56940.18251.06050.04060.03470.0352-0.25930.01250.0472-0.1423-0.05990.04520.14860.04170.01160.16470.02640.2848-5.03-28.853826.5797
20.94230.34830.14520.72010.310.5802-0.04270.27080.0568-0.41250.1964-0.3699-0.55030.51010.19440.6839-0.44540.2660.358-0.0120.45248.493327.549346.2152
30.8522-0.0523-0.08560.85340.08121.3462-0.1288-0.0125-0.0132-0.0175-0.00540.0822-0.0824-0.2288-0.28480.1829-0.03290.10940.1936-0.04220.1287-24.924412.407287.1263
40.89590.14790.56280.95040.2231.90680.1006-0.19850.02070.0994-0.12830.28010.1435-0.3213-0.02360.22360.037-0.08310.3784-0.1480.2353-47.7615.080630.9194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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