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- PDB-9d1p: Lucilia cuprina alpha esterase 7 directed evolution round 5 -

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Basic information

Entry
Database: PDB / ID: 9d1p
TitleLucilia cuprina alpha esterase 7 directed evolution round 5
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: 1.5 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 5
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)66,92610
Polymers65,8871
Non-polymers1,0399
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.952, 91.835, 105.177
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: 65886.547 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 , 6 types, 563 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
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: 1.5→49.01 Å / Num. obs: 90286 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.038 / Rrim(I) all: 0.137 / Χ2: 1.04 / Net I/σ(I): 10.9 / Num. measured all: 1192327
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.2 % / Redundancy: 13.3 % / Rmerge(I) obs: 2.308 / Num. measured all: 58472 / Num. unique obs: 4412 / CC1/2: 0.537 / Rpim(I) all: 0.65 / Rrim(I) all: 2.399 / Χ2: 0.99 / Net I/σ(I) obs: 1.3

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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: 1.5→49.01 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1823 4612 5.11 %
Rwork0.1576 --
obs0.1589 90193 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 69 554 5213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.948
X-RAY DIFFRACTIONf_dihedral_angle_d10.707747
X-RAY DIFFRACTIONf_chiral_restr0.058693
X-RAY DIFFRACTIONf_plane_restr0.008847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.31441510.29532806X-RAY DIFFRACTION99
1.52-1.530.3071430.26522791X-RAY DIFFRACTION99
1.53-1.550.26611300.24292825X-RAY DIFFRACTION99
1.55-1.570.25611530.23372822X-RAY DIFFRACTION99
1.57-1.590.26341520.21852783X-RAY DIFFRACTION99
1.59-1.620.24561660.21742799X-RAY DIFFRACTION99
1.62-1.640.2051450.1982813X-RAY DIFFRACTION99
1.64-1.660.19281430.18872857X-RAY DIFFRACTION100
1.66-1.690.22571640.18582790X-RAY DIFFRACTION99
1.69-1.720.19921570.17392813X-RAY DIFFRACTION99
1.72-1.750.18961490.16922810X-RAY DIFFRACTION100
1.75-1.780.21651470.16312857X-RAY DIFFRACTION100
1.78-1.810.20371570.17162837X-RAY DIFFRACTION100
1.81-1.850.20071620.16352805X-RAY DIFFRACTION100
1.85-1.890.20351540.16672845X-RAY DIFFRACTION100
1.89-1.930.1821470.15692854X-RAY DIFFRACTION100
1.93-1.980.16711410.14912820X-RAY DIFFRACTION100
1.98-2.040.1781470.14442863X-RAY DIFFRACTION100
2.04-2.10.17271660.14622840X-RAY DIFFRACTION100
2.1-2.160.20291550.14742866X-RAY DIFFRACTION100
2.16-2.240.16231710.14722841X-RAY DIFFRACTION100
2.24-2.330.17491520.14612857X-RAY DIFFRACTION100
2.33-2.440.18191300.15372895X-RAY DIFFRACTION100
2.44-2.560.18621580.15522865X-RAY DIFFRACTION100
2.56-2.730.1811480.16042882X-RAY DIFFRACTION100
2.73-2.940.16641660.16692897X-RAY DIFFRACTION100
2.94-3.230.15891570.15642900X-RAY DIFFRACTION100
3.23-3.70.15511670.13832910X-RAY DIFFRACTION100
3.7-4.660.14471570.12972953X-RAY DIFFRACTION100
4.66-49.010.20851770.1593085X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.3541 Å / Origin y: -4.8507 Å / Origin z: -16.663 Å
111213212223313233
T0.1237 Å20.0139 Å2-0.0012 Å2-0.1248 Å20.0055 Å2--0.1272 Å2
L0.4225 °20.1037 °2-0.1076 °2-0.4422 °2-0.0062 °2--0.3562 °2
S0.0262 Å °-0.0079 Å °0.0256 Å °0.0174 Å °-0.0076 Å °0.0299 Å °-0.0137 Å °-0.019 Å °-0 Å °
Refinement TLS groupSelection details: all

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