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- PDB-6g1u: Crystal structure of Torpedo Californica acetylcholinesterase in ... -

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Basic information

Entry
Database: PDB / ID: 6g1u
TitleCrystal structure of Torpedo Californica acetylcholinesterase in complex with 9-Amino-6-chloro-1,2,3,4-tetrahydro-10-methylacridin-10-ium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Torpedo Californica acetylcholinesterase / AD / alzheimer disease
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / 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-E1K / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsCoquelle, N. / Colletier, J.P.
CitationJournal: Molecules / Year: 2018
Title: Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis.
Authors: Galdeano, C. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Bartolini, M. / Perez, B. / Clos, M.V. / Silman, I. / Jean, L. / Colletier, J.P. / Renard, P.Y. / Munoz-Torrero, D.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionApr 4, 2018ID: 6FOT
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 2.0May 1, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jul 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 2.2Jan 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
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,90827
Polymers127,5282
Non-polymers4,38025
Water18,9161050
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,90827
Polymers127,5282
Non-polymers4,38025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area5070 Å2
ΔGint2 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.431, 106.600, 150.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 9 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 63763.965 Da / Num. of mol.: 2 / 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-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: obtained synthetically / 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, 1068 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-E1K / 6-chloranyl-10-methyl-1,2,3,4-tetrahydroacridin-10-ium-9-amine


Mass: 247.743 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H16ClN2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1050 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 200/50 mM MES pH 6.0 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→45.715 Å / Num. obs: 138453 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.9
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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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: 2XI4

2xi4


Resolution: 1.79→45.72 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 6922 5.02 %
Rwork0.18 --
obs0.181 137974 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8469 0 287 1050 9806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069200
X-RAY DIFFRACTIONf_angle_d0.85312522
X-RAY DIFFRACTIONf_dihedral_angle_d12.2225403
X-RAY DIFFRACTIONf_chiral_restr0.0521294
X-RAY DIFFRACTIONf_plane_restr0.0051597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.81030.40052160.36714328X-RAY DIFFRACTION99
1.8103-1.83160.39872380.3464315X-RAY DIFFRACTION100
1.8316-1.8540.33922100.31634364X-RAY DIFFRACTION99
1.854-1.87740.32072360.2824304X-RAY DIFFRACTION100
1.8774-1.90210.28641970.25654345X-RAY DIFFRACTION99
1.9021-1.92820.29052350.24934295X-RAY DIFFRACTION99
1.9282-1.95580.24432150.23094348X-RAY DIFFRACTION99
1.9558-1.98490.28492190.23344345X-RAY DIFFRACTION100
1.9849-2.0160.27962170.21934350X-RAY DIFFRACTION99
2.016-2.0490.25022380.21254319X-RAY DIFFRACTION99
2.049-2.08430.25942250.20094297X-RAY DIFFRACTION99
2.0843-2.12220.23432200.20024361X-RAY DIFFRACTION99
2.1222-2.16310.23032330.19034299X-RAY DIFFRACTION99
2.1631-2.20720.19462080.18934340X-RAY DIFFRACTION100
2.2072-2.25520.22132210.19174379X-RAY DIFFRACTION100
2.2552-2.30770.21992160.17824365X-RAY DIFFRACTION100
2.3077-2.36540.22032490.17744340X-RAY DIFFRACTION100
2.3654-2.42930.2192160.17464383X-RAY DIFFRACTION100
2.4293-2.50080.20582000.17384385X-RAY DIFFRACTION100
2.5008-2.58150.22552570.17584367X-RAY DIFFRACTION100
2.5815-2.67380.23222330.17754359X-RAY DIFFRACTION100
2.6738-2.78080.18822500.1774350X-RAY DIFFRACTION100
2.7808-2.90740.22042320.18374391X-RAY DIFFRACTION100
2.9074-3.06060.20892370.18024393X-RAY DIFFRACTION99
3.0606-3.25230.20742370.17364338X-RAY DIFFRACTION98
3.2523-3.50330.20232440.16784403X-RAY DIFFRACTION100
3.5033-3.85570.18492550.14884405X-RAY DIFFRACTION100
3.8557-4.41330.14642420.13294464X-RAY DIFFRACTION100
4.4133-5.55870.17822320.13864503X-RAY DIFFRACTION100
5.5587-45.73020.20482940.18324617X-RAY DIFFRACTION99

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