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- PDB-9d1m: Lucilia cuprina alpha esterase 7 directed evolution round 2 -

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Basic information

Entry
Database: PDB / ID: 9d1m
TitleLucilia cuprina alpha esterase 7 directed evolution round 2
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 / Carboxylic ester hydrolase
Function and homology information
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 2
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

Downloads & links

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,00212
Polymers66,0651
Non-polymers93711
Water11,782654
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.299, 92.306, 105.634
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: 66064.820 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→46.15 Å / Num. obs: 138352 / % possible obs: 98.7 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.164 / Χ2: 1.02 / Net I/σ(I): 8.7 / Num. measured all: 1829559
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 96.8 % / Redundancy: 13.3 % / Rmerge(I) obs: 3.048 / Num. measured all: 88299 / Num. unique obs: 6624 / CC1/2: 0.428 / Rpim(I) all: 0.858 / Rrim(I) all: 3.168 / Χ2: 0.89 / Net I/σ(I) obs: 0.9

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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: 1.3→45.84 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 6847 4.96 %
Rwork0.1599 --
obs0.1616 138104 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 62 654 5308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.906
X-RAY DIFFRACTIONf_dihedral_angle_d9.95775
X-RAY DIFFRACTIONf_chiral_restr0.082712
X-RAY DIFFRACTIONf_plane_restr0.008863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.38072350.34294175X-RAY DIFFRACTION96
1.31-1.330.36472040.33644281X-RAY DIFFRACTION97
1.33-1.350.34972130.30354270X-RAY DIFFRACTION97
1.35-1.360.31882300.28684278X-RAY DIFFRACTION97
1.36-1.380.29262270.26544299X-RAY DIFFRACTION97
1.38-1.40.28462180.2514266X-RAY DIFFRACTION97
1.4-1.420.27992460.23594307X-RAY DIFFRACTION97
1.42-1.440.26742180.21854273X-RAY DIFFRACTION98
1.44-1.460.26152230.21224303X-RAY DIFFRACTION98
1.46-1.490.27082610.20454328X-RAY DIFFRACTION98
1.49-1.510.25672230.21084290X-RAY DIFFRACTION98
1.51-1.540.21392080.18984358X-RAY DIFFRACTION98
1.54-1.570.23742390.16914315X-RAY DIFFRACTION98
1.57-1.60.19982140.1634343X-RAY DIFFRACTION98
1.6-1.640.18182030.16154363X-RAY DIFFRACTION98
1.64-1.680.23422420.15654368X-RAY DIFFRACTION98
1.68-1.720.19292350.15164336X-RAY DIFFRACTION99
1.72-1.760.16722270.14774399X-RAY DIFFRACTION99
1.76-1.820.19832310.15394343X-RAY DIFFRACTION98
1.82-1.870.2052260.16334414X-RAY DIFFRACTION99
1.87-1.940.22460.16564370X-RAY DIFFRACTION99
1.94-2.020.19972160.15684417X-RAY DIFFRACTION99
2.02-2.110.18822310.15744407X-RAY DIFFRACTION99
2.11-2.220.18842270.15054448X-RAY DIFFRACTION99
2.22-2.360.15442160.14794467X-RAY DIFFRACTION100
2.36-2.540.18742680.15254443X-RAY DIFFRACTION100
2.54-2.80.1772080.1564536X-RAY DIFFRACTION100
2.8-3.210.17282530.14524499X-RAY DIFFRACTION100
3.21-4.040.1642220.1274599X-RAY DIFFRACTION100
4.04-45.840.17262370.13964762X-RAY DIFFRACTION100

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