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- PDB-9d1s: Lucilia cuprina alpha esterase 7 directed evolution round 8 -

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Basic information

Entry
Database: PDB / ID: 9d1s
TitleLucilia cuprina alpha esterase 7 directed evolution round 8
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / directed evolution / insecticide resistance
Function / homologyHydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold / ACETATE ION / Carboxylic ester hydrolase
Function and homology information
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFrkic, R.L. / Fraser, N. / Mabbitt, P.D. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Lucilia cuprina alpha esterase 7 directed evolution round 8
Authors: Frkic, R.L. / Fraser, N. / Correy, G.J. / Mabbitt, P.D. / Jackson, C.J.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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)67,14916
Polymers65,9111
Non-polymers1,23915
Water9,854547
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.245, 92.132, 104.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxylic ester hydrolase


Mass: 65910.555 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 562 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 8-13% (w/v) polyethylene glycol (PEG) 3350, 200 mM BisTris pH 6.5, 6% methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.35→49.23 Å / Num. obs: 124080 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.042 / Rrim(I) all: 0.156 / Χ2: 1.01 / Net I/σ(I): 11.4 / Num. measured all: 1668785
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 99.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 2.886 / Num. measured all: 83043 / Num. unique obs: 6033 / CC1/2: 0.428 / Rpim(I) all: 0.797 / Rrim(I) all: 2.996 / Χ2: 1.03 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→44.56 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1777 6230 5.03 %
Rwork0.1435 --
obs0.1452 123977 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 82 547 5203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.925
X-RAY DIFFRACTIONf_dihedral_angle_d10.537764
X-RAY DIFFRACTIONf_chiral_restr0.081707
X-RAY DIFFRACTIONf_plane_restr0.007864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.29631860.26913852X-RAY DIFFRACTION99
1.37-1.380.27251980.25723893X-RAY DIFFRACTION100
1.38-1.40.28612230.24613858X-RAY DIFFRACTION99
1.4-1.420.25242170.23413857X-RAY DIFFRACTION100
1.42-1.430.27881970.21983862X-RAY DIFFRACTION100
1.43-1.450.24072040.21683928X-RAY DIFFRACTION100
1.45-1.480.24212170.20963853X-RAY DIFFRACTION100
1.48-1.50.25421940.19723885X-RAY DIFFRACTION100
1.5-1.520.24852110.18593875X-RAY DIFFRACTION100
1.52-1.550.20611990.16973905X-RAY DIFFRACTION100
1.55-1.570.23392070.16323891X-RAY DIFFRACTION100
1.57-1.60.18972120.15413883X-RAY DIFFRACTION100
1.6-1.630.18022280.13533881X-RAY DIFFRACTION100
1.63-1.660.18252120.12693940X-RAY DIFFRACTION100
1.66-1.70.191980.12133886X-RAY DIFFRACTION100
1.7-1.740.16312300.11823885X-RAY DIFFRACTION100
1.74-1.780.15552110.1183903X-RAY DIFFRACTION100
1.78-1.830.17521890.12543931X-RAY DIFFRACTION100
1.83-1.890.18472100.12963920X-RAY DIFFRACTION100
1.89-1.950.17561990.12473934X-RAY DIFFRACTION100
1.95-2.020.17642130.12673936X-RAY DIFFRACTION100
2.02-2.10.1752220.12393908X-RAY DIFFRACTION100
2.1-2.190.16682270.12783906X-RAY DIFFRACTION100
2.19-2.310.15652030.13043946X-RAY DIFFRACTION100
2.31-2.450.1581880.13523969X-RAY DIFFRACTION100
2.45-2.640.17011990.1423992X-RAY DIFFRACTION100
2.64-2.910.18872230.14763979X-RAY DIFFRACTION100
2.91-3.330.15972160.14133985X-RAY DIFFRACTION100
3.33-4.190.14971920.12354079X-RAY DIFFRACTION100
4.19-44.560.16052050.1474225X-RAY DIFFRACTION100

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