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- PDB-2xui: CRYSTAL STRUCTURE OF MACHE-Y337A-TZ2PA6 SYN COMPLEX (1 WK) -

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Basic information

Entry
Database: PDB / ID: 2xui
TitleCRYSTAL STRUCTURE OF MACHE-Y337A-TZ2PA6 SYN COMPLEX (1 WK)
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / HYDROLASE FOLD / CLICK CHEMISTRY
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis ...acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / laminin binding / side of membrane / synapse assembly / collagen binding / neuromuscular junction / response to insulin / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / hydrolase activity / cell adhesion / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / 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, tetramerisation domain / Acetylcholinesterase tetramerisation domain / 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
Chem-TZ5 / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / 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 / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)121,5397
Polymers119,3452
Non-polymers2,1955
Water3,549197
1
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9844
Polymers59,6721
Non-polymers1,3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5553
Polymers59,6721
Non-polymers8832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.397, 110.697, 227.830
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(0.7321, -0.403, -0.5492), (-0.4066, -0.9054, 0.1223), (-0.5465, 0.1338, -0.8267)1.139, 24.06, -13.13
2given(0.7321, -0.403, -0.5492), (-0.4066, -0.9054, 0.1223), (-0.5465, 0.1338, -0.8267)1.139, 24.06, -13.13
3given(0.7321, -0.403, -0.5492), (-0.4066, -0.9054, 0.1223), (-0.5465, 0.1338, -0.8267)1.139, 24.06, -13.13
4given(0.7321, -0.403, -0.5492), (-0.4066, -0.9054, 0.1223), (-0.5465, 0.1338, -0.8267)1.139, 24.06, -13.13

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Components

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Protein , 1 types, 2 molecules AB

#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 / Description: LAMBDA-FIX CDNA, GENOMIC DNA / Organ: BRAIN (CDNA) / Plasmid: LAMBDA-ZAP / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 200 molecules

#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-TZ5 / 3,8-DIAMINO-6-PHENYL-5-[6-[1-[2-[(1,2,3,4-TETRAHYDRO-9-ACRIDINYL)AMINO]ETHYL]-1H-1,2,3-TRIAZOL-5-YL]HEXYL]-PHENANTHRIDINIUM


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


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 368 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 368 TO ALA
Sequence detailsEXPRESSED REGION IS RESIDUES 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 25-35% (V/V) PEG 600 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: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 61576 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 66.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.6 / % possible all: 98.6

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Processing

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

1j06


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.291 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23491 1248 2 %RANDOM
Rwork0.19161 ---
obs0.19245 60135 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.941 Å2
Baniso -1Baniso -2Baniso -3
1-4.7 Å20 Å20 Å2
2--3.04 Å20 Å2
3----7.73 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8316 0 157 197 8670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.97711958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17351064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00922.843394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5651573
X-RAY DIFFRACTIONr_chiral_restr0.0950.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226882
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_it0.5421.55331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06728588
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77233416
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0264.53370
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
1A1956medium positional0.10.5
2B1956medium positional0.10.5
1A1874loose positional0.375
2B1874loose positional0.375
1A1956medium thermal0.52
2B1956medium thermal0.52
1A1874loose thermal0.7710
2B1874loose thermal0.7710
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 89 -
Rwork0.283 4171 -
obs--98.36 %
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)
11.21130.04540.211.1389-0.25292.3752-0.0071-0.0647-0.07150.06680.0170.07080.2331-0.2056-0.00990.0453-0.01230.02090.02560.02080.065927.509812.16317.0113
21.1723-0.3410.09521.73130.4742.66430.11810.1496-0.15130.0364-0.09050.09070.1844-0.039-0.02760.0705-0.0314-0.02550.0862-0.0550.09637.80284.2608-40.4215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 541
2X-RAY DIFFRACTION2B4 - 541

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