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- PDB-6uqz: Crystal structure of ChoE D285N mutant in complex with acetate an... -

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Basic information

Entry
Database: PDB / ID: 6uqz
TitleCrystal structure of ChoE D285N mutant in complex with acetate and thiocholine
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
ACETATE ION / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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
Revision 1.4Nov 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)63,4436
Polymers63,0852
Non-polymers3594
Water11,710650
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7223
Polymers31,5421
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7223
Polymers31,5421
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.616, 81.629, 81.383
Angle α, β, γ (deg.)90.000, 99.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ChoE


Mass: 31542.309 Da / Num. of mol.: 2 / Fragment: UNP residues 21-307 / Mutation: D285N
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


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.: 2 / Source method: obtained synthetically / Formula: C5H14NS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 48.01 % / Mosaicity: 0.16 °
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: Aug 8, 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: 1.43→80.17 Å / Num. obs: 104293 / % possible obs: 96.4 % / Redundancy: 3.4 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Rsym value: 0.047 / Net I/av σ(I): 9.9 / Net I/σ(I): 13.3
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
1.43-1.513.10.531.542760137690.3570.6430.532.287.3
1.51-1.63.40.3412.350795147300.2170.4060.3413.598.9
1.6-1.713.30.2183.545487136090.140.260.218597.1
1.71-1.853.50.1365.645405129570.0860.1610.1367.799.1
1.85-2.023.40.0838.938993116070.0530.0990.08311.696.6
2.02-2.263.50.0531337788107720.0340.0630.05318.398.7
2.26-2.613.40.04315.43121892510.0270.0510.04322.696.5
2.61-3.23.50.03417.72825780220.0210.040.03429.598.6
3.2-4.523.40.02920.72068161440.0180.0340.02937.197.3
4.52-81.6293.40.02721.21164934320.0170.0320.02737.397.9

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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: 1.43→80.17 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.467 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 5189 5 %RANDOM
Rwork0.171 ---
obs0.1723 99062 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.69 Å2 / Biso mean: 20.865 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20.56 Å2
2---1.55 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.43→80.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 22 650 5130
Biso mean--30.24 33.37 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0154656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174005
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.7556348
X-RAY DIFFRACTIONr_angle_other_deg0.6151.7299387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.88219.494257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91215637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2521549
X-RAY DIFFRACTIONr_chiral_restr0.0940.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
LS refinement shellResolution: 1.43→1.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 296 -
Rwork0.301 6048 -
all-6344 -
obs--79.32 %

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