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- PDB-1q84: Crystal structure of the mouse acetylcholinesterase-TZ2PA6 anti c... -

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Basic information

Entry
Database: PDB / ID: 1q84
TitleCrystal structure of the mouse acetylcholinesterase-TZ2PA6 anti complex
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / SERINE ESTERASE / ACETYLCHOLINESTERASE / bifunctional inhibitor
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / 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 / 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-TZ4 / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsBourne, Y. / Kolb, H.C. / Radic, Z. / Sharpless, K.B. / Taylor, P. / Marchot, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Freeze-frame inhibitor captures acetylcholinesterase in a unique conformation.
Authors: Bourne, Y. / Kolb, H.C. / Radic, Z. / Sharpless, K.B. / Taylor, P. / Marchot, P.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 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.end_auth_comp_id

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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)129,6497
Polymers127,6002
Non-polymers2,0485
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.272, 111.765, 227.171
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
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTRPTRPAA16 - 5647 - 87
21GLNGLNTRPTRPBB16 - 5647 - 87
32LEULEUASPASPAA60 - 7491 - 105
42LEULEUASPASPBB60 - 7491 - 105
53PHEPHEGLYGLYAA80 - 256111 - 287
63PHEPHEGLYGLYBB80 - 256111 - 287
74ASNASNASNASNAA265 - 490296 - 521
84ASNASNASNASNBB265 - 490296 - 521
95GLNGLNLEULEUAA508 - 539539 - 570
105GLNGLNLEULEUBB508 - 539539 - 570

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 63800.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ACHE / Cell line (production host): HEK 293 / 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
#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-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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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: 3.94 Å3/Da / Density % sol: 68.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 25-32% PEG 600, 20-100 mM Hepes, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-32 %(v/v)PEG6001reservoir
220-100 mMHEPES1reservoirpH6.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 74834 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 57 Å2 / Rsym value: 0.057 / Net I/σ(I): 9.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 549476 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.013 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21404 1507 2 %RANDOM
Rwork0.18427 ---
obs0.18487 73140 99.69 %-
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: 38.036 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å20 Å20 Å2
2--3.04 Å20 Å2
3----6.36 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8314 0 147 338 8799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218732
X-RAY DIFFRACTIONr_bond_other_d0.0020.027822
X-RAY DIFFRACTIONr_angle_refined_deg1.51.96811939
X-RAY DIFFRACTIONr_angle_other_deg1.1318073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42151063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029808
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021891
X-RAY DIFFRACTIONr_nbd_refined0.2010.21716
X-RAY DIFFRACTIONr_nbd_other0.2340.28833
X-RAY DIFFRACTIONr_nbtor_other0.0860.25020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.55327
X-RAY DIFFRACTIONr_mcangle_it1.25928580
X-RAY DIFFRACTIONr_scbond_it2.00333405
X-RAY DIFFRACTIONr_scangle_it3.4514.53359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2866tight positional0.040.05
4563loose positional0.415
2866tight thermal0.120.5
4563loose thermal1.3610
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 102
Rwork0.264 5256
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)
10.8644-0.17440.11320.6311-0.34391.4504-0.0566-0.0184-0.0325-0.00970.01840.02970.2033-0.08210.03820.04060.00850.00640.01490.03860.106927.896112.181716.5564
20.577-0.06130.08660.8190.50091.99120.10360.0857-0.07490.0758-0.09820.05650.1460.0281-0.00540.0939-0.0007-0.02290.0937-0.06240.13217.94824.5817-40.6097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 54132 - 572
2X-RAY DIFFRACTION2BB4 - 54035 - 571
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 2 % / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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