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- PDB-6uqw: Crystal structure of ChoE in complex with acetate and thiocholine -

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Basic information

Entry
Database: PDB / ID: 6uqw
TitleCrystal structure of ChoE in complex with acetate and thiocholine
ComponentsChoEChoi (Korean surname)
KeywordsHYDROLASE / esterase / acetylcholine
Function / homologyGDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / cholinesterase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPham, V.D. / Shi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)183530 Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural insights into the putative bacterial acetylcholinesterase ChoE and its substrate inhibition mechanism.
Authors: Pham, V.D. / To, T.A. / Gagne-Thivierge, C. / Couture, M. / Lague, P. / Yao, D. / Picard, M.E. / Lortie, L.A. / Attere, S.A. / Zhu, X. / Levesque, R.C. / Charette, S.J. / Shi, R.
History
DepositionOct 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)63,6578
Polymers63,0872
Non-polymers5716
Water10,683593
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9355
Polymers31,5431
Non-polymers3924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7233
Polymers31,5431
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.810, 81.760, 81.360
Angle α, β, γ (deg.)90.000, 99.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ChoE / Choi (Korean surname)


Mass: 31543.293 Da / Num. of mol.: 2 / Fragment: UNP residues 21-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (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, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ETM / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL


Mass: 120.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.32 % / Mosaicity: 0.67 °
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: 15% PEG20000, 0.1 M 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
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.65→80.173 Å / Num. all: 68456 / Num. obs: 68456 / % possible obs: 96.5 % / Redundancy: 3.2 % / Rpim(I) all: 0.067 / Rrim(I) all: 0.123 / Rsym value: 0.103 / Net I/av σ(I): 4.9 / Net I/σ(I): 7.6 / Num. measured all: 220070
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
1.65-1.743.20.4591.332265100910.2990.550.4592.597.9
1.74-1.843.10.3571.52853192650.2410.4330.3573.394.8
1.84-1.973.20.2612.22782087340.1720.3140.2614.495.1
1.97-2.133.30.173.62746984350.110.2030.176.398.1
2.13-2.333.20.125.12411975840.0790.1450.128.596.3
2.33-2.613.30.0946.52242967730.0610.1130.09410.295.2
2.61-3.013.40.0757.92088762260.0480.0890.07511.998.6
3.01-3.693.10.0698.41547450030.0460.0830.06913.294.1
3.69-5.223.40.0648.61388641060.040.0760.06415.899.1
5.22-42.5533.20.04210.4719022390.0270.050.04216.296.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6UQV

6uqv


Resolution: 1.65→42.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.634 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 3371 4.9 %RANDOM
Rwork0.185 ---
obs0.187 65063 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.95 Å2 / Biso mean: 16.494 Å2 / Biso min: 5.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20.41 Å2
2---1 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.65→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 35 593 5066
Biso mean--28.29 27.04 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0154600
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173961
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.766259
X-RAY DIFFRACTIONr_angle_other_deg0.5391.749271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06919.482251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98815621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6131548
X-RAY DIFFRACTIONr_chiral_restr0.0780.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 253 -
Rwork0.256 4910 -
all-5163 -
obs--97.99 %

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