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- PDB-2xud: Crystal structure of the Y337A mutant of mouse acetylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 2xud
TitleCrystal structure of the Y337A mutant of mouse acetylcholinesterase
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / HYDROLASE FOLD
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
ACETATE ION / DECAMETHONIUM ION / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBourne, Y. / Radic, Z. / Taylor, P. / Marchot, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Conformational Remodeling of Femtomolar Inhibitor-Acetylcholinesterase Complexes in the Crystalline State
Authors: Bourne, Y. / Radic, Z. / Taylor, P. / Marchot, P.
History
DepositionOct 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 12, 2021Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn / struct_site
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag ..._pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0046
Polymers119,3452
Non-polymers6594
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.424, 109.015, 227.839
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

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
12LEULEUASPASPAA60 - 7460 - 74
22LEULEUASPASPBB60 - 7460 - 74
13PHEPHEVALVALAA80 - 25580 - 255
23PHEPHEVALVALBB80 - 25580 - 255
14ASPASPASNASNAA266 - 490266 - 490
24ASPASPASNASNBB266 - 490266 - 490
15GLNGLNLEULEUAA508 - 539508 - 539
25GLNGLNLEULEUBB508 - 539508 - 539

NCS oper:
IDCodeMatrixVector
1given(0.7448, -0.4048, -0.5305), (-0.4119, -0.9043, 0.1118), (-0.525, 0.1352, -0.8403)1.033, 23.5, -13.97
2given(0.7448, -0.4048, -0.5305), (-0.4119, -0.9043, 0.1118), (-0.525, 0.1352, -0.8403)1.033, 23.5, -13.97
3given(0.7448, -0.4048, -0.5305), (-0.4119, -0.9043, 0.1118), (-0.525, 0.1352, -0.8403)1.033, 23.5, -13.97
4given(0.7448, -0.4048, -0.5305), (-0.4119, -0.9043, 0.1118), (-0.525, 0.1352, -0.8403)1.033, 23.5, -13.97
5given(0.7448, -0.4048, -0.5305), (-0.4119, -0.9043, 0.1118), (-0.525, 0.1352, -0.8403)1.033, 23.5, -13.97

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Components

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 59672.395 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DECAMATHONIUM PARTIALLY BOUND IN CHAIN A / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BLACK6CBA CROSS F1 / Organ: BRAIN (CDNA) / Plasmid: LAMBDA-ZAP, LAMBDA-FIX CDNA, GENOMIC DNA / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS / Cell line (production host): HEK / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-DME / DECAMETHONIUM ION


Mass: 258.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H38N2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 368 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 368 TO ALA
Has protein modificationY
Nonpolymer detailsACETATE (ACT): FAVORABLE DISTANCE TO BE COVALENTLY LINKED TO CATALYTIC SERINE DI(HYDROXYETHYL)ETHER ...ACETATE (ACT): FAVORABLE DISTANCE TO BE COVALENTLY LINKED TO CATALYTIC SERINE DI(HYDROXYETHYL)ETHER (P6G): PARTIALLY ORDERED PEG MOLECULE DECAMETHONIUM ION (DME): PARTIALLY BOUND TO CHAIN A
Sequence detailsEXPRESSED REGION 32-574

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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: 4.08 Å3/Da / Density % sol: 69.6 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM PEG-600 25-35% (V/V) IN 50-100 MM HEPES, PH 6.0-7.0, OR WITH PEG-550 MME 30% (V/V) IN 50 MM NA ACETATE, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 57806 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 57.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.23 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22768 1176 2 %RANDOM
Rwork0.19338 ---
obs0.19407 56261 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.587 Å2
Baniso -1Baniso -2Baniso -3
1-4.16 Å20 Å20 Å2
2--2.35 Å20 Å2
3----6.51 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8309 0 45 186 8540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228635
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9611794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82351066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87522.778396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.131151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.321575
X-RAY DIFFRACTIONr_chiral_restr0.1070.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226773
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5451.55345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05228604
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.733290
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8624.53189
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 84 -
Rwork0.243 4036 -
obs--99.47 %
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)
10.84040.05530.14610.9335-0.1532.2817-0.0165-0.04-0.07220.08180.00350.0640.2085-0.17810.0130.0306-0.01610.01080.01960.01470.051626.905911.846516.8244
20.96-0.35040.18491.43690.30462.50290.13380.1156-0.1251-0.0833-0.07770.0970.2141-0.0188-0.05610.0783-0.018-0.03280.0614-0.03980.06947.88154.3664-40.7166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 542
2X-RAY DIFFRACTION2B4 - 540

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