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- PDB-8d90: Crystal structure of ChoE N147A mutant in complex with bromide ions -

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Basic information

Entry
Database: PDB / ID: 8d90
TitleCrystal structure of ChoE N147A mutant in complex with bromide ions
ComponentsChoE
KeywordsHYDROLASE / esterase
Function / homology: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / cholinesterase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / extracellular region / BROMIDE ION / ChoE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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
Revision 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: ChoE
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,38319
Polymers63,0012
Non-polymers1,38317
Water10,413578
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,23210
Polymers31,5001
Non-polymers7319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1529
Polymers31,5001
Non-polymers6518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.316, 81.710, 80.576
Angle α, β, γ (deg.)90.000, 98.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ChoE


Mass: 31500.266 Da / Num. of mol.: 2 / Mutation: N147A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.34 Å3/Da / Density % sol: 47.41 % / Mosaicity: 0.25 °
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: 15% PEG 20000, 0.1M 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: 0.91988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91988 Å / Relative weight: 1
ReflectionResolution: 1.82→79.586 Å / Num. all: 50495 / Num. obs: 50495 / % possible obs: 97.2 % / Redundancy: 6.9 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Rsym value: 0.1 / Net I/av σ(I): 6.7 / Net I/σ(I): 14.1 / Num. measured all: 347981
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
1.82-1.926.80.8170.94702068890.3630.9620.8172.391.6
1.92-2.037.10.4991.54991770180.2180.5870.4993.998.2
2.03-2.186.70.2842.74396065710.130.340.2846.397.5
2.18-2.357.10.2023.74387461490.090.2420.2029.198.8
2.35-2.576.90.1534.73927156920.070.1860.15311.598.5
2.57-2.886.90.0947.43533951340.0450.1190.09417.197.9
2.88-3.326.90.0610.93158245450.030.0790.0624.598.8
3.32-4.076.80.04114.92624338750.0210.0550.04134.998.3
4.07-5.766.70.038141979229710.0220.0570.03837.698
5.76-44.7596.70.03515.31098316510.0240.0620.03537.597.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UQV

6uqv


Resolution: 1.82→44.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.664 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 2446 4.8 %RANDOM
Rwork0.1681 ---
obs0.1702 48028 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.28 Å2 / Biso mean: 23.071 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å20.26 Å2
2---2.09 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.82→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 27 578 5057
Biso mean--39.05 32.32 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174153
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6396303
X-RAY DIFFRACTIONr_angle_other_deg1.4241.579573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4220.567282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79415685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1541548
X-RAY DIFFRACTIONr_chiral_restr0.0770.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021090
LS refinement shellResolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 151 -
Rwork0.277 3151 -
all-3302 -
obs--86.26 %

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