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- PDB-9d1r: Lucilia cuprina alpha esterase 7 directed evolution round 7 -

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Basic information

Entry
Database: PDB / ID: 9d1r
TitleLucilia cuprina alpha esterase 7 directed evolution round 7
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 / DI(HYDROXYETHYL)ETHER / Carboxylic ester hydrolase
Function and homology information
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 7
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)66,97815
Polymers65,8971
Non-polymers1,08114
Water12,755708
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.369, 92.356, 105.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 65896.516 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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.9 %
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: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→44.68 Å / Num. obs: 177793 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Χ2: 1.05 / Net I/σ(I): 17.1 / Num. measured all: 2290949
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 99.6 % / Redundancy: 9.9 % / Rmerge(I) obs: 2.218 / Num. measured all: 85498 / Num. unique obs: 8671 / CC1/2: 0.467 / Rpim(I) all: 0.73 / Rrim(I) all: 2.339 / Χ2: 0.94 / Net I/σ(I) obs: 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: 1.2→44.68 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1672 8916 5.03 %
Rwork0.1464 --
obs0.1475 177396 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 71 708 5371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.928
X-RAY DIFFRACTIONf_dihedral_angle_d10.661780
X-RAY DIFFRACTIONf_chiral_restr0.086716
X-RAY DIFFRACTIONf_plane_restr0.008880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.29532900.27995533X-RAY DIFFRACTION99
1.21-1.230.30212980.28835543X-RAY DIFFRACTION100
1.23-1.240.24852940.23075608X-RAY DIFFRACTION100
1.24-1.260.29932940.25855422X-RAY DIFFRACTION98
1.26-1.280.34913110.28775532X-RAY DIFFRACTION99
1.28-1.290.22333000.19935532X-RAY DIFFRACTION100
1.29-1.310.26312670.22325609X-RAY DIFFRACTION100
1.31-1.330.23882960.19335585X-RAY DIFFRACTION100
1.33-1.350.21252890.17675572X-RAY DIFFRACTION100
1.35-1.370.23342740.20055568X-RAY DIFFRACTION100
1.37-1.40.21913060.17445596X-RAY DIFFRACTION100
1.4-1.420.17732840.14145630X-RAY DIFFRACTION100
1.42-1.450.17133000.14645542X-RAY DIFFRACTION100
1.45-1.480.16492910.13775585X-RAY DIFFRACTION100
1.48-1.510.14722760.1235626X-RAY DIFFRACTION100
1.51-1.550.1742970.13965587X-RAY DIFFRACTION100
1.55-1.590.14013090.11525580X-RAY DIFFRACTION100
1.59-1.630.13922970.125616X-RAY DIFFRACTION100
1.63-1.680.15763340.1235571X-RAY DIFFRACTION100
1.68-1.730.17112920.1315641X-RAY DIFFRACTION100
1.73-1.790.15412850.12445610X-RAY DIFFRACTION100
1.79-1.860.1533030.12695616X-RAY DIFFRACTION100
1.86-1.950.16662960.14115664X-RAY DIFFRACTION100
1.95-2.050.1662980.14145613X-RAY DIFFRACTION100
2.05-2.180.16142790.14085670X-RAY DIFFRACTION100
2.18-2.350.1653050.13975660X-RAY DIFFRACTION100
2.35-2.590.15863320.14855661X-RAY DIFFRACTION100
2.59-2.960.17533150.15525721X-RAY DIFFRACTION100
2.96-3.730.15162810.13855794X-RAY DIFFRACTION100
3.73-44.680.14823230.13755993X-RAY DIFFRACTION100

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