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

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Basic information

Entry
Database: PDB / ID: 2xup
TitleCRYSTAL STRUCTURE OF the MACHE-Y337A mutant in complex with soaked TZ2PA6 SYN inhibitor
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / HYDROLASE FOLD / CLICK CHEMISTRY
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / 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 ...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
SULFITE ION / Chem-TZ5 / 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 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 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _chem_comp.pdbx_synonyms
Revision 1.5Dec 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 1.6Oct 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)121,5539
Polymers119,3452
Non-polymers2,2097
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.743, 110.001, 227.661
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(0.733, -0.3962, -0.553), (-0.3954, -0.9096, 0.1276), (-0.5535, 0.1251, -0.8234)0.8793, 24.42, -13.32
2given(0.733, -0.3962, -0.553), (-0.3954, -0.9096, 0.1276), (-0.5535, 0.1251, -0.8234)0.8793, 24.42, -13.32
3given(0.733, -0.3962, -0.553), (-0.3954, -0.9096, 0.1276), (-0.5535, 0.1251, -0.8234)0.8793, 24.42, -13.32
4given(0.733, -0.3962, -0.553), (-0.3954, -0.9096, 0.1276), (-0.5535, 0.1251, -0.8234)0.8793, 24.42, -13.32

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Components

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Protein / Sugars , 2 types, 4 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
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
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 4 types, 44 molecules

#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-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#5: 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


Mass: 18.015 Da / Num. of mol.: 39 / 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
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: 55109 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 65.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8

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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: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.785 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23209 1121 2 %RANDOM
Rwork0.2026 ---
obs0.20322 53810 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.338 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å2-0 Å2-0 Å2
2--4.14 Å20 Å2
3----7.54 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8368 0 142 39 8549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.98812250
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55551078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04422.915398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.748151261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.41572
X-RAY DIFFRACTIONr_chiral_restr0.0920.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227081
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_it0.4831.55389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93728688
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3933565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4194.53561
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
1A1869loose positional0.455
2B1869loose positional0.455
1A1959medium thermal0.42
2B1959medium thermal0.42
1A1869loose thermal0.6210
2B1869loose thermal0.6210
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 82 -
Rwork0.314 3851 -
obs--99.72 %
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)
11.4448-0.16290.10431.1693-0.25712.3321-0.0597-0.0479-0.068-0.00480.02790.07160.2214-0.16390.03170.0462-0.00810.01440.02940.03210.069527.747111.846316.4906
21.3771-0.25590.23911.67210.57353.27690.17690.1272-0.18380.1044-0.08770.08030.26360.0926-0.08920.1107-0.0058-0.04630.0838-0.07860.10688.384.5328-40.8037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 543
2X-RAY DIFFRACTION2B4 - 543

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