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- PDB-2xuq: CRYSTAL STRUCTURE OF the MACHE-Y337A mutant in complex with soake... -

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Basic information

Entry
Database: PDB / ID: 2xuq
TitleCRYSTAL STRUCTURE OF the MACHE-Y337A mutant in complex with soaked TZ2PA6 ANTI-SYN inhibitors
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / HYDROLASE FOLD / CLICK CHEMISTRY
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
Chem-TZ4 / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 20, 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_site
Item: _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id ..._pdbx_database_status.status_code_sf / _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 1.5Nov 13, 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)120,9515
Polymers119,3452
Non-polymers1,6063
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.600, 109.700, 227.939
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(0.7323, -0.4038, -0.5483), (-0.4051, -0.9056, 0.1258), (-0.5473, 0.13, -0.8268)0.946, 24.23, -13.73
2given(0.7323, -0.4038, -0.5483), (-0.4051, -0.9056, 0.1258), (-0.5473, 0.13, -0.8268)0.946, 24.23, -13.73
3given(0.7323, -0.4038, -0.5483), (-0.4051, -0.9056, 0.1258), (-0.5473, 0.13, -0.8268)0.946, 24.23, -13.73
4given(0.7323, -0.4038, -0.5483), (-0.4051, -0.9056, 0.1258), (-0.5473, 0.13, -0.8268)0.946, 24.23, -13.73

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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
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BLACK6CBA CROSS F1 / Organ: BRAIN (CDNA) / Plasmid: LAMBDA-ZAP / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#2: 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
#3: Chemical ChemComp-TZ4 / 3,8-DIAMINO-6-PHENYL-5-[6-[1-[2-[(1,2,3,4-TETRAHYDRO-9-ACRIDINYL)AMINO]ETHYL]-1H-1,2,3-TRIAZOL-4-YL]HEXYL]-PHENANTHRIDINIUM


Mass: 661.860 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H45N8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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

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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: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 54760 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 68.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 24.582 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1117 2 %RANDOM
Rwork0.20127 ---
obs0.20215 53502 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.051 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å2-0 Å20 Å2
2--4.03 Å2-0 Å2
3----7.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 119 58 8502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.97211954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92751068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2922.872397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.197151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4141573
X-RAY DIFFRACTIONr_chiral_restr0.0940.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226897
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_it0.5271.55340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02728612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4333403
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5374.53340
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1954medium positional0.120.5
2B1954medium positional0.120.5
1A1847loose positional0.395
2B1847loose positional0.395
1A1954medium thermal0.512
2B1954medium thermal0.512
1A1847loose thermal0.6910
2B1847loose thermal0.6910
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 73 -
Rwork0.326 3792 -
obs--99.33 %
Refinement TLS params.Method: refined / Origin x: 17.813 Å / Origin y: 8.1815 Å / Origin z: -12.0503 Å
111213212223313233
T0.0817 Å2-0.0262 Å20.0074 Å2-0.0217 Å2-0.0075 Å2--0.0956 Å2
L0.5551 °2-0.0846 °20.8399 °2-0.1373 °20.1626 °2--2.2162 °2
S0.0421 Å °0.0262 Å °-0.1196 Å °0.0129 Å °-0.042 Å °0.0575 Å °0.2235 Å °-0.0622 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 541
2X-RAY DIFFRACTION1B4 - 541

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