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- PDB-6xyu: Update of AChE from Drosophila Melanogaster complex with tacrine ... -

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Basic information

Entry
Database: PDB / ID: 6xyu
TitleUpdate of AChE from Drosophila Melanogaster complex with tacrine derivative 9-(3-iodobenzylamino)-1,2,3,4-tetrahydroacridine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / insect / inhibitor / complex
Function / homology
Function and homology information


Neurotransmitter clearance / Synthesis of PC / Aspirin ADME / choline catabolic process / sulfate binding / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / choline metabolic process / acetylcholine catabolic process ...Neurotransmitter clearance / Synthesis of PC / Aspirin ADME / choline catabolic process / sulfate binding / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / choline metabolic process / acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / chemical synaptic transmission / synapse / protein homodimerization activity / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
Acetylcholinesterase, insect / : / 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, insect / : / 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
9-(3-IODOBENZYLAMINO)-1,2,3,4-TETRAHYDROACRIDINE / IODIDE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsNachon, F. / Sussman, J.L.
CitationJournal: Molecules / Year: 2020
Title: A Second Look at the Crystal Structures ofDrosophila melanogasterAcetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of ...Title: A Second Look at the Crystal Structures ofDrosophila melanogasterAcetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of Specific Insecticides.
Authors: Nachon, F. / Rosenberry, T.L. / Silman, I. / Sussman, J.L.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionMar 18, 2020ID: 1QON
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0May 5, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7824
Polymers64,6541
Non-polymers1,1283
Water2,774154
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9777
Polymers129,3092
Non-polymers1,6695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)94.910, 94.910, 160.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-837-

HOH

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 64654.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ace, CG17907 / Plasmid: S2-SEC 1/3 / Cell line (production host): SCHNEIDER LINE 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07140, acetylcholinesterase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-I40 / 9-(3-IODOBENZYLAMINO)-1,2,3,4-TETRAHYDROACRIDINE


Mass: 414.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19IN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 55.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 13% MPEG2000, 0.1 M ammonium sulfate, 0.03 M leucine, 0.1 M acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→42.45 Å / Num. obs: 24909 / % possible obs: 96.64 % / Redundancy: 2.8 % / Biso Wilson estimate: 52.05 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0635 / Rpim(I) all: 0.0412 / Rrim(I) all: 0.0766 / Net I/σ(I): 10.97
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 2458 / CC1/2: 0.763 / CC star: 0.93 / Rpim(I) all: 0.358 / Rrim(I) all: 0.638 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata processing
XSCALEdata scaling
PHASERphasing
PHENIX1.16_3549refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qon

1qon
PDB Unreleased entry


Resolution: 2.51→42.45 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.4005
RfactorNum. reflection% reflection
Rfree0.2523 870 3.5 %
Rwork0.1858 --
obs0.1882 24877 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.71 Å2
Refinement stepCycle: LAST / Resolution: 2.51→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 0 154 4447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814419
X-RAY DIFFRACTIONf_angle_d0.96446020
X-RAY DIFFRACTIONf_chiral_restr0.0551634
X-RAY DIFFRACTIONf_plane_restr0.0077781
X-RAY DIFFRACTIONf_dihedral_angle_d5.16242573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.670.3971440.31943949X-RAY DIFFRACTION97.78
2.67-2.870.32711460.27364031X-RAY DIFFRACTION98.96
2.87-3.160.3121470.23074045X-RAY DIFFRACTION99.24
3.16-3.620.25961450.18164024X-RAY DIFFRACTION97.86
3.62-4.560.21421440.15633971X-RAY DIFFRACTION95.59
4.56-42.450.22011440.15383987X-RAY DIFFRACTION91.09
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)
12.16291245274-0.7747968640910.8948322446032.43046258876-0.420658209613.433256319920.03409682377430.2227173776750.0547378752208-0.403663755803-0.1015980729660.00828598112535-0.2852356990870.3426458849110.09433727331260.397314894327-0.007768477381170.009320129627580.38582158843-0.01063159467550.37238538738819.980066340664.64056770020.158818410022
21.97853300143-0.2251667226380.730445860642.536047049330.5806063449473.88711347959-0.194921910142-0.0792244905340.1409103283470.07622586312620.0958825209259-0.299368191299-0.5158736603450.5520020133960.1177526551150.382985494192-0.01022678308320.01028559309440.5309927772450.004631862399590.4014071100231.527358533664.472716251522.1139942028
31.92304842818-0.01479349866670.8921682331842.074689976080.1558223198524.32208965175-0.172013855238-0.254406519047-0.2838740489630.2545801558350.1660912409780.05479302877030.50298008670.229740664289-0.07144650016970.3283287433780.03623267096670.05624771291090.4177109848060.09605824580640.41820792120525.927149377451.271981116523.8179593442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 351 )
2X-RAY DIFFRACTION2chain 'A' and (resid 352 through 499 )
3X-RAY DIFFRACTION3chain 'A' and (resid 500 through 573 )

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