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- PDB-8d8z: Crystal structure of ChoE N147A mutant in complex with thiocholin... -

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Basic information

Entry
Database: PDB / ID: 8d8z
TitleCrystal structure of ChoE N147A mutant in complex with thiocholine and chloride
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
2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 1.2Nov 20, 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)63,4968
Polymers63,0012
Non-polymers4966
Water11,998666
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7484
Polymers31,5001
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7484
Polymers31,5001
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.673, 81.800, 81.099
Angle α, β, γ (deg.)90.000, 99.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
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: 0.17 °
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: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.38→79.968 Å / Num. all: 110159 / Num. obs: 110159 / % possible obs: 91.6 % / Redundancy: 3.4 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Rsym value: 0.036 / Net I/av σ(I): 13.7 / Net I/σ(I): 16.6 / Num. measured all: 375233
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
1.38-1.453.40.5891.357055166480.3710.6990.589295.2
1.45-1.543.40.3742.154009158730.2380.4450.3743.495.8
1.54-1.653.40.2243.451510150950.1420.2660.2245.396.6
1.65-1.783.50.1425.449421141530.0890.1680.1428.197.6
1.78-1.953.30.0858.936903113540.0560.1020.08512.684.8
1.95-2.183.50.04815.634736100290.030.0570.04821.582.9
2.18-2.523.30.03121.82969389270.020.0370.03131.183.8
2.52-3.093.50.02426.62838981600.0150.0280.02441.990.3
3.09-4.363.40.019322054761220.0120.0220.01955.587.2
4.36-81.83.40.01732.31297037980.0110.0210.01759.297

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Processing

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

6uqv


Resolution: 1.38→35.95 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.276 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0604 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2 5476 5 %RANDOM
Rwork0.1678 ---
obs0.1694 104631 91.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.15 Å2 / Biso mean: 19.699 Å2 / Biso min: 8.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å2-0 Å20.14 Å2
2---1.17 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 1.38→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 28 666 5146
Biso mean--39.34 32.43 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174208
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6396349
X-RAY DIFFRACTIONr_angle_other_deg1.5551.579695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07120.426282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93515690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0071549
X-RAY DIFFRACTIONr_chiral_restr0.0920.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021098
LS refinement shellResolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 412 -
Rwork0.279 7937 -
all-8349 -
obs--93.83 %

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