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- PDB-8d91: Crystal structure of ChoE in complex with acetate and tetraethyla... -

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Basic information

Entry
Database: PDB / ID: 8d91
TitleCrystal structure of ChoE in complex with acetate and tetraethylammonium (TEA)
ComponentsChoEChoi (Korean surname)
KeywordsHYDROLASE / esterase
Function / homologyGDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / cholinesterase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / TETRAETHYLAMMONIUM ION / ChoE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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

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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)63,4656
Polymers63,0872
Non-polymers3794
Water8,755486
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7333
Polymers31,5431
Non-polymers1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7333
Polymers31,5431
Non-polymers1892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.653, 81.850, 81.311
Angle α, β, γ (deg.)90.000, 99.610, 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 (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-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-NET / TETRAETHYLAMMONIUM ION / Tetraethylammonium


Mass: 130.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H20N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 277 K / Method: microbatch / Details: 16% PEG 6000, 0.01M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.49→80.17 Å / Num. all: 90356 / Num. obs: 90356 / % possible obs: 94.2 % / Redundancy: 3.2 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Rsym value: 0.035 / Net I/av σ(I): 12.3 / Net I/σ(I): 15.7 / Num. measured all: 288016
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
1.49-1.572.50.3652.128368113860.2890.4690.3652.281.3
1.57-1.673.30.2662.942824128770.1720.3190.2663.997.7
1.67-1.783.40.1754.441139121600.1120.2080.1755.897.9
1.78-1.923.20.0886.935701110650.060.1070.0889.395.3
1.92-2.113.30.0779.833883102210.050.0920.07712.696.2
2.11-2.363.10.04411.72763489770.0310.0540.04420.993.3
2.36-2.723.40.03320.22788182940.0210.0390.03327.597.3
2.72-3.333.30.02523.72300669970.0160.030.02535.796.9
3.33-4.713.30.02325.11733053170.0150.0280.02344.595.2
4.71-40.9253.30.0226.11025030620.0130.0240.0244.497.9

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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: 1.49→40.12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.099 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0853 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 4323 4.9 %RANDOM
Rwork0.1974 ---
obs0.1986 84446 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.87 Å2 / Biso mean: 25.269 Å2 / Biso min: 10.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å2-0 Å20.55 Å2
2---1.08 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.49→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 26 486 4960
Biso mean--37.35 34.55 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174161
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.6446272
X-RAY DIFFRACTIONr_angle_other_deg1.6371.5839578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85820.536280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03415679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6071548
X-RAY DIFFRACTIONr_chiral_restr0.110.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021083
LS refinement shellResolution: 1.49→1.529 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 260 -
Rwork0.241 5063 -
all-5323 -
obs--75.45 %
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)
10.1941-0.0805-0.07910.68880.07250.19120.0041-0.0168-0.0169-0.04450.01030.013-0.0161-0.0106-0.01440.008-0.0013-0.01590.0801-0.00490.0751-14.4074-0.214137.6242
20.2052-0.0307-0.01290.20860.27410.7385-0.04170.0111-0.0126-0.0266-0.03630.0115-0.0092-0.06250.0780.1080.00930.00680.0404-0.01280.028-7.9854-29.3173-0.1708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 501
2X-RAY DIFFRACTION2B21 - 501

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