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- PDB-5tym: alpha-esterase-7 in complex with [3-bromo-5-(pyrrolidin-1-yl)phen... -

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Basic information

Entry
Database: PDB / ID: 5tym
Titlealpha-esterase-7 in complex with [3-bromo-5-(pyrrolidin-1-yl)phenyl]borinic 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
[3-bromo-5-(pyrrolidin-1-yl)phenyl]borinic acid / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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

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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)66,6672
Polymers66,4131
Non-polymers2541
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.145, 100.789, 223.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 66412.922 Da / Num. of mol.: 1 / Mutation: D83A, K530E
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-7NS / [3-bromo-5-(pyrrolidin-1-yl)phenyl]borinic acid


Mass: 253.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13BBrNO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 100 mM sodium acetate pH 5.1, 15% 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: Sep 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→38 Å / Num. obs: 48767 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rsym value: 0.14 / Net I/σ(I): 12.4
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 10.9 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1.1 / Num. unique all: 4823 / CC1/2: 0.326 / % 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: 1.84→38.017 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2872 2512 5.15 %
Rwork0.2279 --
obs0.2309 48767 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→38.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 14 117 4688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084695
X-RAY DIFFRACTIONf_angle_d1.0866355
X-RAY DIFFRACTIONf_dihedral_angle_d14.4171761
X-RAY DIFFRACTIONf_chiral_restr0.042677
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.87540.44621180.37162588X-RAY DIFFRACTION100
1.8754-1.91370.39781500.3462482X-RAY DIFFRACTION99
1.9137-1.95530.39461300.33072565X-RAY DIFFRACTION100
1.9553-2.00080.37791470.31252517X-RAY DIFFRACTION100
2.0008-2.05080.37371340.29932538X-RAY DIFFRACTION100
2.0508-2.10630.36291520.28412523X-RAY DIFFRACTION100
2.1063-2.16820.34071480.28362548X-RAY DIFFRACTION100
2.1682-2.23820.35051260.26722593X-RAY DIFFRACTION100
2.2382-2.31820.32551580.26192496X-RAY DIFFRACTION100
2.3182-2.4110.33561390.26442563X-RAY DIFFRACTION100
2.411-2.52070.29261460.24892547X-RAY DIFFRACTION100
2.5207-2.65360.34121230.2462591X-RAY DIFFRACTION100
2.6536-2.81980.27471460.24272553X-RAY DIFFRACTION100
2.8198-3.03740.34461520.24332556X-RAY DIFFRACTION100
3.0374-3.34290.2761380.22682604X-RAY DIFFRACTION100
3.3429-3.82620.2741300.2042613X-RAY DIFFRACTION100
3.8262-4.81910.20971360.17692633X-RAY DIFFRACTION100
4.8191-38.02510.2131390.1732745X-RAY DIFFRACTION99

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