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- PDB-6uqv: Crystal structure of ChoE, a bacterial acetylcholinesterase from ... -

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Basic information

Entry
Database: PDB / ID: 6uqv
TitleCrystal structure of ChoE, a bacterial acetylcholinesterase from Pseudomonas aeruginosa
ComponentsChoE
KeywordsHYDROLASE / esterase / acetylcholine / prokaryotic / acetylcholinesterase
Function / homologyGDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / cholinesterase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / extracellular region / butanoic acid / ChoE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsShi, R. / Pham, V.D. / To, T.A.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2376
Polymers31,5431
Non-polymers6935
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint7 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.157, 109.673, 84.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-404-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ChoE


Mass: 31543.293 Da / Num. of mol.: 1 / 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 , 6 types, 408 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BUA / BUTANOIC ACID


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 3.01 Å3/Da / Density % sol: 59.1 % / Mosaicity: 0.19 °
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: 25% PEG8000, 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: 1.35→65.754 Å / Num. all: 82957 / Num. obs: 82957 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Rsym value: 0.05 / Net I/av σ(I): 9.3 / Net I/σ(I): 17.2 / Num. measured all: 526567
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
1.35-1.425.60.8166425118190.3640.8830.82.298
1.42-1.516.60.5281.574812113640.220.5730.5283.799.7
1.51-1.616.30.3322.367471107200.1420.3620.3325.699.8
1.61-1.746.60.2063.766556100170.0850.2230.2068.799.9
1.74-1.916.30.1216.25827892380.0520.1320.12113.399.7
1.91-2.136.70.06710.65604883590.0280.0720.06722.799.8
2.13-2.466.30.04614.24689874180.020.050.04631.799.8
2.46-3.026.60.03815.94180862980.0160.0410.03841.299.9
3.02-4.276.30.02821.23084449130.0120.030.02851.399.7
4.27-51.8286.20.02621.91742728110.0110.0280.02652.999.5

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→41.11 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.898 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.045
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 4212 5.1 %RANDOM
Rwork0.1536 ---
obs0.1547 78707 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.57 Å2 / Biso mean: 19.96 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å2-0 Å2
2--1.13 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.35→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 44 403 2676
Biso mean--35.07 35.62 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0152420
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172087
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.7693296
X-RAY DIFFRACTIONr_angle_other_deg0.7411.7524913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.1319.203138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.34915334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6841528
X-RAY DIFFRACTIONr_chiral_restr0.130.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 281 -
Rwork0.273 5620 -
all-5901 -
obs--96.52 %

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