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

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Basic information

Entry
Database: PDB / ID: 6arx
TitleCrystal structure of an insecticide-resistant acetylcholinesterase mutant from the malaria vector Anopheles gambiae in the ligand-free state
ComponentsAcetylcholinesterase
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


choline metabolic process / acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / synapse / extracellular space / plasma membrane
Similarity search - Function
: / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...: / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / 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
CITRATE ANION / Acetylcholinesterase
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)122,69110
Polymers121,2362
Non-polymers1,4558
Water6,485360
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,69110
Polymers121,2362
Non-polymers1,4558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area3400 Å2
ΔGint-8 kcal/mol
Surface area41450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.599, 149.599, 225.857
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

#1: Protein Acetylcholinesterase / AChE


Mass: 60617.965 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
#2: 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


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
#3: Chemical
ChemComp-FLC / CITRATE ANION


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


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


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
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: 6.02 Å3/Da / Density % sol: 79.56 % / Mosaicity: 0.35 °
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: 2.3→200 Å / Num. obs: 125913 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 46.63 Å2
Data reduction details: high redundancy of data and CC1/2 0.3 was used for resolution cut-off
Rmerge(I) obs: 0.21 / Rpim(I) all: 0.077 / Rrim(I) all: 0.224 / Χ2: 1.023 / Net I/σ(I): 3.1 / Num. measured all: 1027353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.346.52.63462610.3631.092.8590.53399.6
2.34-2.387.92.56663220.4710.9672.7450.534100
2.38-2.438.32.2662280.5650.8292.4090.54100
2.43-2.488.42.08962980.6470.762.2250.548100
2.48-2.538.41.76863280.6550.6421.8830.557100
2.53-2.598.41.5462130.7440.561.640.556100
2.59-2.668.31.30563360.7820.4771.3910.577100
2.66-2.7381.04162850.8460.3891.1120.605100
2.73-2.817.40.82262710.8850.3220.8840.613100
2.81-2.980.69562990.9040.2590.7430.637100
2.9-38.70.55562950.9360.1980.590.663100
3-3.128.70.42163120.9610.1510.4470.759100
3.12-3.268.60.33762950.970.1220.3590.903100
3.26-3.448.40.24562830.9830.090.2611.102100
3.44-3.657.70.18563120.9870.0710.1991.44999.9
3.65-3.938.20.15962970.9890.0590.171.76199.9
3.93-4.338.60.13262880.9920.0480.142.05100
4.33-4.968.30.10963290.9940.040.1172.21100
4.96-6.2480.10263200.9940.0380.1091.85299.8
6.24-2008.40.0763410.9970.0250.0741.82898.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ey4


Resolution: 2.302→49.103 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 6259 4.98 %RANDOM
Rwork0.1777 ---
obs0.179 125762 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.92 Å2 / Biso mean: 54.2164 Å2 / Biso min: 29.61 Å2
Refinement stepCycle: final / Resolution: 2.302→49.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 95 360 8957
Biso mean--94.53 53.82 -
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128935
X-RAY DIFFRACTIONf_angle_d1.16512214
X-RAY DIFFRACTIONf_chiral_restr0.0631297
X-RAY DIFFRACTIONf_plane_restr0.0081616
X-RAY DIFFRACTIONf_dihedral_angle_d11.8795268
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5176X-RAY DIFFRACTION5.377TORSIONAL
12B5176X-RAY DIFFRACTION5.377TORSIONAL
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 (%)
2.3021-2.32830.37381710.34373785395694
2.3283-2.35570.34092260.318639894215100
2.3557-2.38440.31982000.30539714171100
2.3844-2.41460.32141850.294440144199100
2.4146-2.44630.27791830.296239754158100
2.4463-2.47990.31832240.289439624186100
2.4799-2.51530.32072230.286939954218100
2.5153-2.55280.33142500.272439074157100
2.5528-2.59270.29932160.279239994215100
2.5927-2.63520.28471910.261140094200100
2.6352-2.68070.28381820.25340274209100
2.6807-2.72940.2581960.247239944190100
2.7294-2.78190.26022290.235939454174100
2.7819-2.83870.28491970.234139824179100
2.8387-2.90040.27091730.231540154188100
2.9004-2.96780.26541970.225539884185100
2.9678-3.04210.24082200.211140274247100
3.0421-3.12430.2492270.208139954222100
3.1243-3.21620.24112130.212839404153100
3.2162-3.320.24282430.2139804223100
3.32-3.43860.23021920.190339944186100
3.4386-3.57630.23062460.17239654211100
3.5763-3.7390.16912210.160739914212100
3.739-3.9360.17781860.140840094195100
3.936-4.18250.15422120.12940044216100
4.1825-4.50520.132290.11239894218100
4.5052-4.95820.12432250.10839974222100
4.9582-5.67480.14552230.127939774200100
5.6748-7.14610.16151900.139140434233100
7.1461-49.11460.16341890.14984035422499

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