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- PDB-6ary: Crystal structure of an insecticide-resistant acetylcholinesteras... -

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Basic information

Entry
Database: PDB / ID: 6ary
TitleCrystal structure of an insecticide-resistant acetylcholinesterase mutant from the malaria vector Anopheles gambiae in complex with a difluoromethyl ketone inhibitor
ComponentsAcetylcholinesterase
KeywordsHYDROLASE/Hydrolase Inhibitor / hydrolase / difluoromethyl ketone / HYDROLASE-Hydrolase Inhibitor complex
Function / homology
Function and homology information


acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / synapse / extracellular space / plasma membrane
Similarity search - Function
Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BT7 / CITRATE ANION / Acetylcholinesterase
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.257 Å
AuthorsCheung, J. / Mahmood, A. / Kalathur, R. / Lixuan, L. / Carlier, P.R.
CitationJournal: Structure / Year: 2018
Title: Structure of the G119S Mutant Acetylcholinesterase of the Malaria Vector Anopheles gambiae Reveals Basis of Insecticide Resistance.
Authors: Cheung, J. / Mahmood, A. / Kalathur, R. / Liu, L. / Carlier, P.R.
History
DepositionAug 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,18812
Polymers121,2962
Non-polymers1,89210
Water6,990388
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,18812
Polymers121,2962
Non-polymers1,89210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area3410 Å2
ΔGint-10 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.333, 150.333, 226.478
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 163 through 337 or resid 339...
21(chain B and (resid 163 through 337 or resid 339...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEU(chain A and (resid 163 through 337 or resid 339...AA163 - 3373 - 177
12TRPTRPPROPRO(chain A and (resid 163 through 337 or resid 339...AA339 - 351179 - 191
13ARGARGGLNGLN(chain A and (resid 163 through 337 or resid 339...AA353 - 569193 - 409
14TYRTYRALAALA(chain A and (resid 163 through 337 or resid 339...AA571 - 659411 - 499
15GLYGLYASNASN(chain A and (resid 163 through 337 or resid 339...AA661 - 699501 - 539
21ASNASNLEULEU(chain B and (resid 163 through 337 or resid 339...BB163 - 3373 - 177
22TRPTRPPROPRO(chain B and (resid 163 through 337 or resid 339...BB339 - 351179 - 191
23ARGARGGLNGLN(chain B and (resid 163 through 337 or resid 339...BB353 - 569193 - 409
24TYRTYRALAALA(chain B and (resid 163 through 337 or resid 339...BB571 - 659411 - 499
25GLYGLYASNASN(chain B and (resid 163 through 337 or resid 339...BB661 - 699501 - 539

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Acetylcholinesterase / / AChE


Mass: 60647.996 Da / Num. of mol.: 2 / Fragment: residues 162 to 702 / Mutation: G280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: Ace, ACE1, ACHE1, AGAP001356 / Plasmid: modified pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q869C3, acetylcholinesterase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 395 molecules

#2: Chemical ChemComp-BT7 / (1S)-2,2-difluoro-1-[1-(pentan-3-yl)-1H-pyrazol-4-yl]ethan-1-ol


Mass: 218.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16F2N2O
#4: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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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: 6.09 Å3/Da / Density % sol: 79.81 % / Mosaicity: 0.194 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.9 - 1.0M tri-ammonium citrate pH 6.5, 1 - 3% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→200 Å / Num. obs: 134751 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 60.62 Å2
Data reduction details: The redundancy was high from merging of multiple crystals and CC1/2 0.3 was used for resolution cut-off
Rmerge(I) obs: 0.157 / Rpim(I) all: 0.033 / Rrim(I) all: 0.161 / Χ2: 0.973 / Net I/σ(I): 3.7 / Num. measured all: 2982777
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.2912.12.53467420.4150.7392.6510.453100
2.29-2.3313.72.10567220.6130.5732.1880.445100
2.33-2.3815.91.97667290.7050.4992.0420.443100
2.38-2.42171.78767020.7940.4391.8430.451100
2.42-2.4819.11.70467180.8580.3951.7510.463100
2.48-2.5320.91.54967440.8740.3451.5880.467100
2.53-2.622.21.43266820.9120.3111.4660.482100
2.6-2.6723.21.27367750.9380.2731.3020.516100
2.67-2.7524.31.05366790.9540.2191.0760.526100
2.75-2.8324.60.83967350.9730.1740.8570.557100
2.83-2.9424.70.67667560.9780.1390.690.594100
2.94-3.0524.60.49367070.9840.1020.5030.674100
3.05-3.19250.36567530.9890.0740.3720.77100
3.19-3.3625.40.2767070.9940.0550.2750.921100
3.36-3.5725.50.19867520.9960.040.2021.215100
3.57-3.8524.10.1667480.9970.0330.1641.541100
3.85-4.2325.10.13267350.9980.0270.1351.883100
4.23-4.8525.70.10867600.9980.0210.112.087100
4.85-6.1124.50.09767570.9980.020.0991.782100
6.11-20025.20.07468480.9990.0150.0751.90899.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.257→49.299 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.88
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 6662 4.95 %RANDOM
Rwork0.1617 ---
obs0.163 134527 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 69.7615 Å2 / Biso min: 47.01 Å2
Refinement stepCycle: final / Resolution: 2.257→49.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 125 388 9015
Biso mean--98.34 69.99 -
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118967
X-RAY DIFFRACTIONf_angle_d1.06812262
X-RAY DIFFRACTIONf_chiral_restr0.1761299
X-RAY DIFFRACTIONf_plane_restr0.0071618
X-RAY DIFFRACTIONf_dihedral_angle_d11.8585274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5175X-RAY DIFFRACTION3.821TORSIONAL
12B5175X-RAY DIFFRACTION3.821TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2574-2.2830.35091640.32123540370481
2.283-2.30990.35082280.313442564484100
2.3099-2.33810.32661890.299342724461100
2.3381-2.36770.30442310.280942854516100
2.3677-2.39880.29782100.267742834493100
2.3988-2.43170.27492040.263243194523100
2.4317-2.46640.27452350.253242714506100
2.4664-2.50320.28382190.251542684487100
2.5032-2.54230.26922610.231842584519100
2.5423-2.5840.25752270.227342424469100
2.584-2.62860.26532250.225242734498100
2.6286-2.67640.27042190.233943204539100
2.6764-2.72780.23641820.229443314513100
2.7278-2.78350.25872330.219542714504100
2.7835-2.8440.25052320.215642424474100
2.844-2.91020.29331800.222943054485100
2.9102-2.98290.26172280.212543034531100
2.9829-3.06360.24062340.205643014535100
3.0636-3.15370.25582340.20242484482100
3.1537-3.25550.25542370.207242874524100
3.2555-3.37180.23412320.203342614493100
3.3718-3.50680.20182400.174942944534100
3.5068-3.66630.19032670.162242664533100
3.6663-3.85960.18372090.148542864495100
3.8596-4.10130.14312000.129443254525100
4.1013-4.41780.132500.113742924542100
4.4178-4.8620.12622530.106242724525100
4.862-5.56470.12512200.118643124532100
5.5647-7.00770.14722150.129843154530100
7.0077-49.31090.15712040.140743674571100

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