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- PDB-6xys: Update of native acetylcholinesterase from Drosophila Melanogaster -

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Basic information

Entry
Database: PDB / ID: 6xys
TitleUpdate of native acetylcholinesterase from Drosophila Melanogaster
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / insect / catalytic / intermediates
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 / acetylcholine catabolic process / acetylcholinesterase ...Neurotransmitter clearance / Synthesis of PC / Aspirin ADME / choline catabolic process / sulfate binding / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / choline metabolic process / 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, 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 ...Acetylcholinesterase, insect / : / 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
ACETATE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsNachon, F. / Sussman, J.L.
Citation
Journal: 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.
#1: Journal: Protein Sci. / Year: 2000
Title: Three-dimensional structures of Drosophila melanogaster acetylcholinesterase and of its complexes with two potent inhibitors.
Authors: Harel, M. / Kryger, G. / Rosenberry, T.L. / Mallender, W.D. / Lewis, T. / Fletcher, R.J. / Guss, J.M. / Silman, I. / Sussman, J.L.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionMar 18, 2020ID: 1QO9
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / pdbx_struct_special_symmetry / 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.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_special_symmetry.auth_seq_id / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Jan 24, 2024Group: 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
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)65,6604
Polymers64,6541
Non-polymers1,0053
Water1,69394
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4087
Polymers129,3092
Non-polymers1,1005
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)94.620, 94.620, 159.010
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-601-

CL

21A-708-

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 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3-2/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
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: 2.455→34.18 Å / Num. obs: 26803 / % possible obs: 98.54 % / Redundancy: 6 % / Biso Wilson estimate: 51.47 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0487 / Rpim(I) all: 0.0184 / Rrim(I) all: 0.0524 / Net I/σ(I): 20.7
Reflection shellResolution: 2.455→2.543 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2542 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.1848 / Rrim(I) all: 0.387

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Processing

Software
NameVersionClassification
XDSdata processing
XSCALEdata scaling
PHENIX1.16_3549refinement
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qo9

1qo9
PDB Unreleased entry


Resolution: 2.46→34.18 Å / SU ML: 0.4415 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.1301
RfactorNum. reflection% reflection
Rfree0.2962 1338 5 %
Rwork0.2293 --
obs0.2326 26738 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79.57 Å2
Refinement stepCycle: LAST / Resolution: 2.46→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 0 94 4376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824427
X-RAY DIFFRACTIONf_angle_d1.04446026
X-RAY DIFFRACTIONf_chiral_restr0.0564638
X-RAY DIFFRACTIONf_plane_restr0.0072783
X-RAY DIFFRACTIONf_dihedral_angle_d7.68113561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.540.52331260.39942403X-RAY DIFFRACTION95.29
2.54-2.640.44091320.35262504X-RAY DIFFRACTION98.95
2.64-2.760.40931310.33572496X-RAY DIFFRACTION99.02
2.76-2.910.37191340.31612520X-RAY DIFFRACTION99.44
2.91-3.090.3961320.31232521X-RAY DIFFRACTION99.51
3.09-3.330.37371350.28852547X-RAY DIFFRACTION99.59
3.33-3.670.36411340.24692551X-RAY DIFFRACTION99.3
3.67-4.20.27271360.19712576X-RAY DIFFRACTION99.09
4.2-5.280.23171360.16462588X-RAY DIFFRACTION98.8
5.28-34.180.19281420.17362694X-RAY DIFFRACTION97.12
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)
12.64151116185-0.666181915276-0.2307802605462.330948456040.7658561246923.601367331040.4752793648350.3436233877280.167584132732-1.0062510972-0.0360081588838-0.327057577998-0.7755228262011.3245296951-0.1817921604820.763238669117-0.2579318013690.1958610884480.826567492311-0.07057365744070.54304512922326.683032170361.2623939448-7.588984906
22.00663512098-1.14916525731-0.2085349923193.107552874060.5012285140174.514304604450.166911856517-0.0664442315780.128459953861-0.5913727356080.0984358125310.0464663949946-0.8202220039590.844211271534-0.1299499486290.52044343716-0.1632981420380.05392842600180.401222932617-0.08846751367810.46513276992217.70859823161.63068268392.93633376248
31.9120780443-0.7358448390420.1495775172921.9024319294-0.003380079170333.29239754661-0.0454922297043-0.1074845646520.477149062359-0.338386788860.142345459761-0.217559337267-1.520118596740.837245057672-0.08400099814641.04311315059-0.3066593048820.1213161455970.469668827066-0.08268176954060.60049662066317.985427426573.06458792378.27113352555
41.26500677874-0.6170717640760.1477350615241.850585966750.5357447694422.13358492798-0.1498013854-0.1289309030710.2925947895780.04065250047910.514557869005-0.566408645716-0.6560602763961.19182160568-0.2970617091250.63749412634-0.2144509805820.06034351167021.194192492-0.2331374718880.66098445832832.833406539565.215907414922.7448846766
51.671830676430.169132249615-0.110662136361.128025519670.3134453039123.79798431371-0.261955237257-0.351274292507-0.1927325740370.1224182760840.346155792986-0.2167171203110.3684732266551.13074445701-0.2147982816720.3681287093230.1549095699350.03247347045940.979899932052-0.02347503800220.52143303117325.859078109951.385753283823.6717891522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 289 )
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 375 )
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 499 )
5X-RAY DIFFRACTION5chain 'A' and (resid 500 through 573 )

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