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- PDB-2ha6: Crystal structure of mutant S203A of mouse acetylcholinesterase c... -

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Basic information

Entry
Database: PDB / ID: 2ha6
TitleCrystal structure of mutant S203A of mouse acetylcholinesterase complexed with succinylcholine
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
ACETIC ACID / Chem-SCK / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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)121,0018
Polymers119,4972
Non-polymers1,5046
Water11,241624
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.983, 109.825, 227.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical
ChemComp-SCK / 2,2'-[(1,4-DIOXOBUTANE-1,4-DIYL)BIS(OXY)]BIS(N,N,N-TRIMETHYLETHANAMINIUM) / SUCCINYLDICHOLINE


Mass: 290.399 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30N2O4
#3: 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
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
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: 4.13 Å3/Da / Density % sol: 70.24 %
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: ID14-4 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 93560 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.9 / % possible all: 68.3

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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: 2.25→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 10.008 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19832 1805 2 %RANDOM
Rwork0.17721 ---
obs0.17765 87759 94.89 %-
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: 47.036 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2--3.43 Å20 Å2
3----6.12 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8333 0 103 624 9060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228701
X-RAY DIFFRACTIONr_bond_other_d0.0010.025883
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.96711883
X-RAY DIFFRACTIONr_angle_other_deg0.9483.00214204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48751065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5422.947397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.246151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8751571
X-RAY DIFFRACTIONr_chiral_restr0.0810.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021855
X-RAY DIFFRACTIONr_nbd_refined0.2030.21831
X-RAY DIFFRACTIONr_nbd_other0.2030.26262
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24194
X-RAY DIFFRACTIONr_nbtor_other0.0880.24375
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2462
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7661.55691
X-RAY DIFFRACTIONr_mcbond_other0.1991.52147
X-RAY DIFFRACTIONr_mcangle_it1.14128603
X-RAY DIFFRACTIONr_scbond_it1.73733738
X-RAY DIFFRACTIONr_scangle_it2.7054.53280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 98 -
Rwork0.252 4308 -
obs--68.14 %
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)
10.9005-0.05430.02320.7325-0.38891.8603-0.02690.0044-0.02750.02130.02660.01310.1843-0.09790.0003-0.1032-0.01320-0.15850.0311-0.045827.052111.6416.7066
20.6349-0.08580.14480.8490.31782.37140.12360.0619-0.05140.0268-0.08460.04790.1927-0.004-0.039-0.1253-0.0235-0.0266-0.1375-0.0551-0.09547.67944.4494-40.8785
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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