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- PDB-6emi: Crystal structure of a variant of human butyrylcholinesterase exp... -

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Basic information

Entry
Database: PDB / ID: 6emi
TitleCrystal structure of a variant of human butyrylcholinesterase expressed in bacteria.
ComponentsCholinesterase
KeywordsHYDROLASE / alpha-beta hydrolase / prokaryotic expression / dimeric form / disulfide bond.
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / Synthesis of PC / nuclear envelope lumen / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.476 Å
AuthorsBrazzolotto, X. / Igert, A. / Guillon, V. / Santoni, G. / Nachon, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of DefensePDH-2-NRBC-3-C-3201 France
CitationJournal: Molecules / Year: 2017
Title: Bacterial Expression of Human Butyrylcholinesterase as a Tool for Nerve Agent Bioscavengers Development.
Authors: Brazzolotto, X. / Igert, A. / Guillon, V. / Santoni, G. / Nachon, F.
History
DepositionOct 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _software.name
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholinesterase
B: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,72841
Polymers120,2602
Non-polymers3,46839
Water6,774376
1
A: Cholinesterase
hetero molecules

A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,00132
Polymers120,2602
Non-polymers2,74130
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Cholinesterase
hetero molecules

B: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,45450
Polymers120,2602
Non-polymers4,19448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)159.840, 75.170, 122.070
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cholinesterase / Acylcholine acylhydrolase / Butyrylcholine esterase / Choline esterase II / Pseudocholinesterase


Mass: 60129.930 Da / Num. of mol.: 2
Mutation: -3G, -2A, -1M, A7T, S48P, D54G, C66M, Q71T, L110M, I111V, H126P, Q176K, K180D, N188D, K190N, S191R, S215P, F227A, T234M, L236P, Y237E, T250L, L274D, G283S, I305T, N342D, I356V, G360N, ...Mutation: -3G, -2A, -1M, A7T, S48P, D54G, C66M, Q71T, L110M, I111V, H126P, Q176K, K180D, N188D, K190N, S191R, S215P, F227A, T234M, L236P, Y237E, T250L, L274D, G283S, I305T, N342D, I356V, G360N, V377E, D379E, Q380D, E387D, G390A, D391E, N397F, T406A, F409Y, S410A, W412H, F417Y, D454L, A459E, S466E, V468M, K469R, S489Q, S495P, T508S, Q518H, T523N, 530STOP
Source method: isolated from a genetically manipulated source
Details: A and B chains were numbered according to the sequence of the physiological human butyrylcholinaesterase.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06276, cholinesterase

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Non-polymers , 6 types, 415 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.074 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 2.476→65.02 Å / Num. obs: 51072 / % possible obs: 98.37 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1163 / Rpim(I) all: 0.0737 / Rrim(I) all: 0.1381 / Net I/σ(I): 7.92
Reflection shellResolution: 2.476→2.565 Å / Rmerge(I) obs: 0.5303 / Rpim(I) all: 0.3278 / Rrim(I) all: 0.6246

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHASERphasing
autoPROCdata scaling
MxCuBEdata collection
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0I

1p0i


Resolution: 2.476→65.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 2576 5.06 %
Rwork0.222 --
obs0.2237 50941 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.476→65.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8420 0 219 376 9015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038853
X-RAY DIFFRACTIONf_angle_d0.53111939
X-RAY DIFFRACTIONf_dihedral_angle_d12.4486209
X-RAY DIFFRACTIONf_chiral_restr0.0431237
X-RAY DIFFRACTIONf_plane_restr0.0041541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4758-2.52340.32411400.30042700X-RAY DIFFRACTION98
2.5234-2.57490.32751320.28232619X-RAY DIFFRACTION98
2.5749-2.63090.34081220.29422647X-RAY DIFFRACTION98
2.6309-2.69210.29771360.28442696X-RAY DIFFRACTION98
2.6921-2.75940.30151540.27722694X-RAY DIFFRACTION98
2.7594-2.83410.33881410.25752645X-RAY DIFFRACTION99
2.8341-2.91740.26691230.25972679X-RAY DIFFRACTION98
2.9174-3.01160.30441620.24552662X-RAY DIFFRACTION98
3.0116-3.11930.26281490.24152698X-RAY DIFFRACTION99
3.1193-3.24410.29711580.23522660X-RAY DIFFRACTION99
3.2441-3.39180.31271580.22782682X-RAY DIFFRACTION99
3.3918-3.57060.23111520.21592678X-RAY DIFFRACTION99
3.5706-3.79430.25521380.20482703X-RAY DIFFRACTION99
3.7943-4.08720.2531190.19392713X-RAY DIFFRACTION99
4.0872-4.49850.18871600.18522679X-RAY DIFFRACTION98
4.4985-5.14920.19861510.18442726X-RAY DIFFRACTION99
5.1492-6.48670.24021440.21742740X-RAY DIFFRACTION99
6.4867-68.64770.21981370.19342744X-RAY DIFFRACTION96

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