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- PDB-5typ: alpha-esterase-7 in complex with (3-bromo-4-methylphenyl)boronic acid -

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Basic information

Entry
Database: PDB / ID: 5typ
Titlealpha-esterase-7 in complex with (3-bromo-4-methylphenyl)boronic 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-4-methylphenyl)boronic acid / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 13, 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)66,6042
Polymers66,3891
Non-polymers2151
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.464, 101.796, 224.651
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: 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-7NJ / (3-bromo-4-methylphenyl)boronic acid


Mass: 214.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8BBrO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 100 mM sodium acetate pH 5.2, 19% 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: 1.88→37.7 Å / Num. obs: 45621 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.9
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 10.9 % / Rmerge(I) obs: 2.5 / Mean I/σ(I) obs: 1.1 / Num. unique all: 4444 / CC1/2: 0.398 / % possible all: 98.3

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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: 1.88→37.715 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2833 2267 4.97 %
Rwork0.2204 --
obs0.2234 45621 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→37.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 11 129 4697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094696
X-RAY DIFFRACTIONf_angle_d1.1636359
X-RAY DIFFRACTIONf_dihedral_angle_d14.7681752
X-RAY DIFFRACTIONf_chiral_restr0.049676
X-RAY DIFFRACTIONf_plane_restr0.006820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.92090.47021370.41662565X-RAY DIFFRACTION97
1.9209-1.96560.41991410.38292641X-RAY DIFFRACTION99
1.9656-2.01470.35881390.32732729X-RAY DIFFRACTION100
2.0147-2.06920.37851250.29712650X-RAY DIFFRACTION100
2.0692-2.13010.3751470.28962672X-RAY DIFFRACTION100
2.1301-2.19880.30921270.27962715X-RAY DIFFRACTION100
2.1988-2.27740.43651470.30652680X-RAY DIFFRACTION100
2.2774-2.36860.2841200.25862719X-RAY DIFFRACTION100
2.3686-2.47630.32371580.2472694X-RAY DIFFRACTION100
2.4763-2.60690.31211510.23662690X-RAY DIFFRACTION100
2.6069-2.77010.28291590.23372690X-RAY DIFFRACTION100
2.7701-2.98390.30121570.23262734X-RAY DIFFRACTION100
2.9839-3.28410.28991450.21712722X-RAY DIFFRACTION100
3.2841-3.75890.2621380.18862772X-RAY DIFFRACTION100
3.7589-4.73440.2061380.16282774X-RAY DIFFRACTION100
4.7344-37.72220.2221380.17092907X-RAY DIFFRACTION100

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