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- PDB-8d8y: Crystal structure of ChoE N147A mutant in complex with acetylthio... -

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Basic information

Entry
Database: PDB / ID: 8d8y
TitleCrystal structure of ChoE N147A mutant in complex with acetylthiocholine
ComponentsChoE
KeywordsHYDROLASE / esterase
Function / homology
Function and homology information


cholinesterase activity
Similarity search - Function
: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYLTHIOCHOLINE / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsPham, V.D. / Shi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)183530 Canada
CitationJournal: To be published
Title: Crystal structures of bacterial acetylcholinesterase ChoE provide insights into the plasticity of catalytic Ser in regulating the active site geometry and the functional state of the SGNH hydrolases
Authors: Pham, V.D. / Couture, M. / Lortie, L.-A. / Picard, M.-E. / Charette, S. / Levesque, R. / Shi, R.
History
DepositionJun 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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: ChoE
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,82110
Polymers63,0012
Non-polymers8208
Water10,665592
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9105
Polymers31,5001
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9105
Polymers31,5001
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.632, 81.786, 81.258
Angle α, β, γ (deg.)90.000, 99.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ChoE


Mass: 31500.266 Da / Num. of mol.: 2 / Mutation: N147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: choE, PA4921 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HUP2

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Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-AT3 / ACETYLTHIOCHOLINE / 2-{[(1S)-1-HYDROXYETHYL]THIO}-N,N,N-TRIMETHYLETHANAMINIUM


Mass: 162.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ETM / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL


Mass: 120.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.13 % / Mosaicity: 0.11 °
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: 25% PEG 8000, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.54→80.064 Å / Num. all: 83290 / Num. obs: 83290 / % possible obs: 96 % / Redundancy: 3.4 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Rsym value: 0.045 / Net I/av σ(I): 10.4 / Net I/σ(I): 14.5 / Num. measured all: 281950
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.54-1.6230.4921.630791103290.3410.6020.4922.481.8
1.62-1.723.50.3362.241425118780.2140.40.3363.899.3
1.72-1.843.40.2073.537364110130.1330.2470.2075.798.1
1.84-1.993.50.1245.936205103610.0780.1470.1249.198.6
1.99-2.183.40.0739.73274195170.0470.0880.07314.398.8
2.18-2.433.40.053132911784860.0340.0630.05319.597.6
2.43-2.813.40.04116.12627176200.0260.0480.04124.398.6
2.81-3.443.40.032192196663770.020.0380.03231.597.9
3.44-4.873.40.02821.51669049480.0180.0330.02838.297.6
4.87-44.9623.40.02620.7938027610.0160.0310.02637.897.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UQV

6uqv


Resolution: 1.54→45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1509 / FOM work R set: 0.8568 / SU B: 1.563 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0725 / SU Rfree: 0.0753 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 4076 4.9 %RANDOM
Rwork0.1536 ---
obs0.1551 79187 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91 Å2 / Biso mean: 22.315 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å2-0 Å20.13 Å2
2---1 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.54→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 48 592 5092
Biso mean--41.59 35.42 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134700
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174278
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.6456412
X-RAY DIFFRACTIONr_angle_other_deg1.5321.589853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47520.314287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46215701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4581551
X-RAY DIFFRACTIONr_chiral_restr0.0930.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021112
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 245 -
Rwork0.269 4523 -
all-4768 -
obs--74.53 %

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