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- PDB-5tyk: alpha-esterase-7 in complex with 3-chloro-4-[(2-fluorophenyl)meth... -

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Basic information

Entry
Database: PDB / ID: 5tyk
Titlealpha-esterase-7 in complex with 3-chloro-4-[(2-fluorophenyl)methoxy]phenylborinic acid
ComponentsCarboxylic ester hydrolase
Keywordshydrolase/hydrolase inhibitor / carboxylesterase / insecticide resistance / covalent inhibitor / organophosphate / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity
Similarity search - Function
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-7N4 / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCorrey, G.J. / Jackson, C.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Overcoming insecticide resistance through computational inhibitor design.
Authors: Correy, G.J. / Zaidman, D. / Harmelin, A. / Carvalho, S. / Mabbitt, P.D. / Calaora, V. / James, P.J. / Kotze, A.C. / Jackson, C.J. / London, N.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6532
Polymers66,3891
Non-polymers2641
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.799, 100.792, 221.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

21A-966-

HOH

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 66388.836 Da / Num. of mol.: 1 / Mutation: D83A, M363L, I419F, A472T, I505T, K530E, D554G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly)
Gene: LcaE7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q25252, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-7N4 / {3-chloro-4-[(2-fluorophenyl)methoxy]phenyl}borinic acid


Mass: 264.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11BClFO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium acetate pH 5.0, 22% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→45.9 Å / Num. obs: 64943 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 1.3 / Num. unique all: 6383 / CC1/2: 0.341 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CH3

5ch3


Resolution: 1.65→45.882 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 3242 4.99 %
Rwork0.187 --
obs0.1888 64943 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→45.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 18 266 4841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074709
X-RAY DIFFRACTIONf_angle_d1.0946375
X-RAY DIFFRACTIONf_dihedral_angle_d13.7951759
X-RAY DIFFRACTIONf_chiral_restr0.045678
X-RAY DIFFRACTIONf_plane_restr0.005823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.67470.34461410.32652596X-RAY DIFFRACTION99
1.6747-1.70090.32751480.30692662X-RAY DIFFRACTION100
1.7009-1.72880.36611490.30112628X-RAY DIFFRACTION100
1.7288-1.75860.30761530.28822659X-RAY DIFFRACTION100
1.7586-1.79050.31591480.26342641X-RAY DIFFRACTION100
1.7905-1.8250.2811220.25072669X-RAY DIFFRACTION100
1.825-1.86220.29311240.23782692X-RAY DIFFRACTION100
1.8622-1.90270.26361380.22492639X-RAY DIFFRACTION100
1.9027-1.9470.22531380.21452649X-RAY DIFFRACTION100
1.947-1.99570.27751590.19752689X-RAY DIFFRACTION100
1.9957-2.04960.24531390.19552613X-RAY DIFFRACTION100
2.0496-2.110.23961550.19452639X-RAY DIFFRACTION100
2.11-2.17810.22281310.18482704X-RAY DIFFRACTION100
2.1781-2.25590.19061470.18652666X-RAY DIFFRACTION100
2.2559-2.34620.22671250.18912671X-RAY DIFFRACTION100
2.3462-2.4530.24371390.18572697X-RAY DIFFRACTION100
2.453-2.58230.2341300.18722684X-RAY DIFFRACTION100
2.5823-2.74410.22861470.18572692X-RAY DIFFRACTION100
2.7441-2.95590.20521310.17712741X-RAY DIFFRACTION100
2.9559-3.25330.20541500.1742692X-RAY DIFFRACTION100
3.2533-3.72390.19321330.16562747X-RAY DIFFRACTION100
3.7239-4.6910.18541420.15162753X-RAY DIFFRACTION100
4.691-45.89920.1931530.16632878X-RAY DIFFRACTION100

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