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- PDB-5hcu: Crystal structure of mouse acetylchoinesterase inhibited by DFP -

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Basic information

Entry
Database: PDB / ID: 5hcu
TitleCrystal structure of mouse acetylchoinesterase inhibited by DFP
ComponentsAcetylcholinesterase
KeywordsHYDROLASE
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 / laminin binding / side of membrane / synaptic cleft / 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
Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4151 Å
AuthorsTran, T.H. / Tong, L.
CitationJournal: Chembiochem / Year: 2015
Title: Discovery of New Classes of Compounds that Reactivate Acetylcholinesterase Inhibited by Organophosphates.
Authors: Katz, F.S. / Pecic, S. / Tran, T.H. / Trakht, I. / Schneider, L. / Zhu, Z. / Ton-That, L. / Luzac, M. / Zlatanic, V. / Damera, S. / Macdonald, J. / Landry, D.W. / Tong, L. / Stojanovic, M.N.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJan 20, 2016ID: 5DTG
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase


Theoretical massNumber of molelcules
Total (without water)119,9412
Polymers119,9412
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-11 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.575, 114.346, 226.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 59970.684 Da / Num. of mol.: 2 / Fragment: UNP residues 32-571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21836, acetylcholinesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% v/v PEG 600, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4151→50 Å / Num. obs: 76507 / % possible obs: 99.8 % / Redundancy: 4.8 % / Net I/σ(I): 7.7
Reflection shellResolution: 2.4151→2.4445 Å / Num. measured obs: 2724 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HA2

2ha2


Resolution: 2.4151→50 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 3968 5.03 %
Rwork0.2057 74968 -
obs0.2071 65006 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.86 Å2 / Biso mean: 60.8917 Å2 / Biso min: 32.66 Å2
Refinement stepCycle: final / Resolution: 2.4151→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8361 0 0 131 8492
Biso mean---55.64 -
Num. residues----1067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118615
X-RAY DIFFRACTIONf_angle_d1.21511765
X-RAY DIFFRACTIONf_chiral_restr0.0571262
X-RAY DIFFRACTIONf_plane_restr0.0091548
X-RAY DIFFRACTIONf_dihedral_angle_d14.3863099
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4840X-RAY DIFFRACTION5.929TORSIONAL
12B4840X-RAY DIFFRACTION5.929TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4151-2.44450.36781340.36142590272498
2.4445-2.47550.36861420.353926512793100
2.4755-2.50810.42551280.319926502778100
2.5081-2.54240.31561430.304826722815100
2.5424-2.57870.31451480.292526162764100
2.5787-2.61720.33881500.286326762826100
2.6172-2.65810.29481360.27326272763100
2.6581-2.70170.29161320.267426552787100
2.7017-2.74830.27691400.257526382778100
2.7483-2.79820.31191340.268826852819100
2.7982-2.8520.31651450.258126392784100
2.852-2.91030.26641530.265126842837100
2.9103-2.97350.27531360.255226102746100
2.9735-3.04270.30171680.245226702838100
3.0427-3.11880.25561320.23726662798100
3.1188-3.20310.28621470.237826542801100
3.2031-3.29730.27341280.242926982826100
3.2973-3.40370.25961310.228326822813100
3.4037-3.52530.26831040.220827072811100
3.5253-3.66640.21981540.197226562810100
3.6664-3.83320.21171400.182126882828100
3.8332-4.03520.22251610.173326772838100
4.0352-4.28780.21251360.166727032839100
4.2878-4.61860.16171450.150127272872100
4.6186-5.08290.18551550.148826802835100
5.0829-5.81710.21351510.168627362887100
5.8171-7.32430.19471350.18527962931100
7.3243-46.23860.17921600.17742835299598
Refinement TLS params.Method: refined / Origin x: 20.9512 Å / Origin y: -8.6213 Å / Origin z: -11.0868 Å
111213212223313233
T0.4298 Å2-0.0437 Å2-0.0079 Å2-0.4008 Å2-0.0032 Å2--0.4358 Å2
L0.2407 °2-0.0803 °2-0.4727 °2-0.1387 °2-0.1366 °2--1.1646 °2
S0.0029 Å °0.0184 Å °0.0733 Å °0.0214 Å °-0.029 Å °-0.0607 Å °-0.1511 Å °0.0415 Å °0.0307 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 540
2X-RAY DIFFRACTION1allB4 - 540
3X-RAY DIFFRACTION1allD1 - 155

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