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- PDB-6uqx: Crystal structure of ChoE in complex with propionylthiocholine -

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Basic information

Entry
Database: PDB / ID: 6uqx
TitleCrystal structure of ChoE in complex with propionylthiocholine
ComponentsChoEChoi (Korean surname)
KeywordsHYDROLASE / esterase
Function / homology
Function and homology information


cholinesterase activity
Similarity search - Function
GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
2-(TRIMETHYLAMMONIUM)ETHYL THIOL / IODIDE ION / PROPANOIC ACID / propionylthiocholine / ChoE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: ChoE
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7117
Polymers63,0872
Non-polymers6245
Water6,197344
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8463
Polymers31,5431
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8654
Polymers31,5431
Non-polymers3213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.599, 81.489, 81.373
Angle α, β, γ (deg.)90.000, 100.110, 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 / 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

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-QFJ / propionylthiocholine / N,N,N-trimethyl-2-(propanoylsulfanyl)ethan-1-aminium


Mass: 176.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ETM / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL


Mass: 120.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.86 % / Mosaicity: 0.27 °
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: Nov 15, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→80.108 Å / Num. all: 49649 / Num. obs: 49649 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Rsym value: 0.15 / Net I/av σ(I): 4.4 / Net I/σ(I): 9.3 / Num. measured all: 338188
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
1.85-1.956.90.9660.84962771990.3951.0450.9662.199.2
1.95-2.076.60.6041.34512868410.2520.6560.6043.199.1
2.07-2.217.10.3931.94530864130.1590.4250.3934.899.4
2.21-2.396.90.3032.44145760260.1240.3280.3036.199.5
2.39-2.626.80.2323.13705154720.0960.2520.2327.699
2.62-2.9370.1574.43522050210.0640.170.15710.799.5
2.93-3.386.60.1046.62907444070.0440.1130.10414.999.1
3.38-4.146.80.0718.72564137480.0290.0770.07122.899.5
4.14-5.856.50.0629.51904029080.0260.0670.0622499.2
5.85-44.896.60.05211.11064216140.0220.0570.05224.798.8

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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: 1.85→40.09 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.483 / SU ML: 0.135 / SU R Cruickshank DPI: 0.1496 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.144
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2361 4.8 %RANDOM
Rwork0.1913 ---
obs0.1935 47260 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.77 Å2 / Biso mean: 27.701 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å2-0 Å21.01 Å2
2---2.14 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: final / Resolution: 1.85→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 25 344 4793
Biso mean--39.1 33.75 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0154588
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173945
X-RAY DIFFRACTIONr_angle_refined_deg1.791.7616248
X-RAY DIFFRACTIONr_angle_other_deg0.6161.7359239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64219.291254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97215623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6351550
X-RAY DIFFRACTIONr_chiral_restr0.0910.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 188 -
Rwork0.297 3480 -
all-3668 -
obs--99.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04780.1752-0.02870.9351-0.17970.0659-0.0016-0.02920.0151-0.05530.00290.07610.00790.0072-0.00140.0706-0.0030.0080.0749-0.00520.1296-14.8229-0.209937.5863
20.2392-0.0854-0.16540.24990.24370.2833-0.00270.0271-0.0358-0.0663-0.03570.0152-0.0771-0.0480.03840.30720.02740.05390.01-0.00770.0414-8.2053-29.3216-0.2863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 403
2X-RAY DIFFRACTION2B23 - 403

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