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- PDB-5tyl: alpha-esterase-7 in complex with naphthalen-2-ylboronic acid -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5tyl
Titlealpha-esterase-7 in complex with naphthalen-2-ylboronic 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
naphthalen-2-ylboronic acid / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 2.0Oct 9, 2019Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _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 2.1Nov 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 2.2Oct 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 2.3Nov 20, 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)66,5612
Polymers66,3891
Non-polymers1721
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.767, 101.399, 223.537
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-872-

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-7N7 / naphthalen-2-ylboronic acid


Mass: 171.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9BO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 100 mM sodium acetate pH 4.8, 22% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→34.546 Å / Num. obs: 56360 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 0.8 / Num. unique all: 5596 / CC1/2: 0.276 / % possible all: 99.9

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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: 1.75→34.546 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 2765 4.91 %
Rwork0.2144 --
obs0.2168 56360 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→34.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 13 194 4764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094696
X-RAY DIFFRACTIONf_angle_d1.0976358
X-RAY DIFFRACTIONf_dihedral_angle_d13.611754
X-RAY DIFFRACTIONf_chiral_restr0.044676
X-RAY DIFFRACTIONf_plane_restr0.005819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78020.46681430.39842611X-RAY DIFFRACTION100
1.7802-1.81250.44191270.36622701X-RAY DIFFRACTION100
1.8125-1.84740.36691170.34812606X-RAY DIFFRACTION100
1.8474-1.88510.38731430.33622664X-RAY DIFFRACTION100
1.8851-1.92610.36151420.31482643X-RAY DIFFRACTION100
1.9261-1.97090.3631370.27662663X-RAY DIFFRACTION100
1.9709-2.02020.28981620.2692631X-RAY DIFFRACTION100
2.0202-2.07480.33551490.25132643X-RAY DIFFRACTION100
2.0748-2.13580.32851610.24912615X-RAY DIFFRACTION100
2.1358-2.20480.3041220.25782691X-RAY DIFFRACTION100
2.2048-2.28360.30811210.24132674X-RAY DIFFRACTION100
2.2836-2.3750.30141500.2352639X-RAY DIFFRACTION100
2.375-2.4830.30481350.22912694X-RAY DIFFRACTION100
2.483-2.61390.33211330.22032684X-RAY DIFFRACTION100
2.6139-2.77760.23851300.21532707X-RAY DIFFRACTION100
2.7776-2.99190.27161360.20542690X-RAY DIFFRACTION100
2.9919-3.29280.24461580.19492707X-RAY DIFFRACTION100
3.2928-3.76880.20191420.17922712X-RAY DIFFRACTION100
3.7688-4.74630.18741260.16122756X-RAY DIFFRACTION100
4.7463-34.55230.20771310.16272864X-RAY DIFFRACTION99

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