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- PDB-2ha7: Crystal structure of mutant S203A of mouse acetylcholinesterase c... -

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Basic information

Entry
Database: PDB / ID: 2ha7
TitleCrystal structure of mutant S203A of mouse acetylcholinesterase complexed with butyrylthiocholine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / HYDROLASE FOLD / SERINE ESTERASE / ACETYLCHOLINESTERASE / MUTANT / HOMODIMER / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / collagen binding / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
2-(BUTYRYLSULFANYL)-N,N,N-TRIMETHYLETHANAMINIUM / butanoic acid / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / IODIDE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.66 Å
AuthorsBourne, Y. / Radic, Z. / Sulzenbacher, G. / Kim, E. / Taylor, P. / Marchot, P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Substrate and product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding
Authors: Bourne, Y. / Radic, Z. / Sulzenbacher, G. / Kim, E. / Taylor, P. / Marchot, P.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 2, 2021Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)121,71918
Polymers119,4972
Non-polymers2,22216
Water4,216234
1
B: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,71918
Polymers119,4972
Non-polymers2,22216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)79.325, 111.115, 228.651
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-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTRPTRPAA16 - 5616 - 56
21GLNGLNTRPTRPBB16 - 5616 - 56
32LEULEUASPASPAA60 - 7460 - 74
42LEULEUASPASPBB60 - 7460 - 74
53PHEPHEVALVALAA80 - 25580 - 255
63PHEPHEVALVALBB80 - 25580 - 255
74ASNASNASNASNAA265 - 490265 - 490
84ASNASNASNASNBB265 - 490265 - 490
95GLNGLNLEULEUAA508 - 539508 - 539
105GLNGLNLEULEUBB508 - 539508 - 539

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59748.488 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: S203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / Variant (production host): LAMBDA ZAP / References: UniProt: P21836, acetylcholinesterase

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Non-polymers , 6 types, 250 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-ETM / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL


Mass: 120.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NS
#4: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-BCH / 2-(BUTYRYLSULFANYL)-N,N,N-TRIMETHYLETHANAMINIUM / BUTYRYLTHIOCHOLINE


Mass: 190.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20NOS
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 4.21 Å3/Da / Density % sol: 70.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25-32% PEG550 MME or PEG600, 60-100mM HEPES or Na acetate, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 57849 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.66→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.74 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24141 1202 2 %RANDOM
Rwork0.19964 ---
obs0.2005 57514 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.794 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--3.6 Å20 Å2
3----6.8 Å2
Refinement stepCycle: LAST / Resolution: 2.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 78 234 8660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.96311835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85651066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73722.861395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.789151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2251572
X-RAY DIFFRACTIONr_chiral_restr0.0870.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.23758
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25882
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4561.55372
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83928610
X-RAY DIFFRACTIONr_scbond_it1.26233676
X-RAY DIFFRACTIONr_scangle_it2.1714.53225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1960medium positional0.110.5
1884loose positional0.385
1960medium thermal0.452
1884loose thermal1.2910
LS refinement shellResolution: 2.657→2.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 76 -
Rwork0.26 4021 -
obs--99.76 %
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)
11.1757-0.002-0.00150.9733-0.40872.6937-0.02970.0045-0.0525-0.05020.01440.05930.1944-0.13670.0154-0.1950.0039-0.0006-0.25790.0175-0.086127.332411.999216.7786
21.00650.1303-0.24511.35870.56713.17930.1189-0.06070.0628-0.1553-0.11080.0385-0.2121-0.0828-0.0081-0.16110.03780.0335-0.1549-0.0675-0.072847.61751.010740.7428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 5421 - 542
2X-RAY DIFFRACTION2BB4 - 5434 - 543

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