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- PDB-9d1o: Lucilia cuprina alpha esterase 7 directed evolution round 4 -

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Basic information

Entry
Database: PDB / ID: 9d1o
TitleLucilia cuprina alpha esterase 7 directed evolution round 4
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: 1.35 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 4
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)66,0524
Polymers65,6621
Non-polymers3893
Water10,413578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.739, 91.582, 105.358
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: 65662.195 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: 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.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
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: 1.35→47.61 Å / Num. obs: 118685 / % possible obs: 99.8 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.034 / Rrim(I) all: 0.121 / Χ2: 1.03 / Net I/σ(I): 11.8 / Num. measured all: 1543895
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 99.4 % / Redundancy: 13.4 % / Rmerge(I) obs: 2.68 / Num. measured all: 77496 / Num. unique obs: 5801 / CC1/2: 0.426 / Rpim(I) all: 0.75 / Rrim(I) all: 2.785 / Χ2: 0.95 / 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: 1.35→47.61 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1877 6059 5.11 %
Rwork0.1513 --
obs0.1531 118572 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 26 578 5123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.934
X-RAY DIFFRACTIONf_dihedral_angle_d8.997704
X-RAY DIFFRACTIONf_chiral_restr0.083688
X-RAY DIFFRACTIONf_plane_restr0.007840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.33872130.29853668X-RAY DIFFRACTION99
1.37-1.380.33182170.26793677X-RAY DIFFRACTION100
1.38-1.40.27342090.25033693X-RAY DIFFRACTION99
1.4-1.420.30072080.2373673X-RAY DIFFRACTION99
1.42-1.430.2851970.22983692X-RAY DIFFRACTION99
1.43-1.450.25852090.21213713X-RAY DIFFRACTION99
1.45-1.480.23042020.19343711X-RAY DIFFRACTION100
1.48-1.50.25252120.19153683X-RAY DIFFRACTION100
1.5-1.520.24132070.1863699X-RAY DIFFRACTION100
1.52-1.550.23862030.17263721X-RAY DIFFRACTION100
1.55-1.570.21771780.16443720X-RAY DIFFRACTION100
1.57-1.60.22411890.15383740X-RAY DIFFRACTION100
1.6-1.630.19222070.14243714X-RAY DIFFRACTION100
1.63-1.660.18022040.13813736X-RAY DIFFRACTION100
1.66-1.70.18412020.13553747X-RAY DIFFRACTION100
1.7-1.740.18322020.12933712X-RAY DIFFRACTION100
1.74-1.780.17621900.1353758X-RAY DIFFRACTION100
1.78-1.830.17451980.13123728X-RAY DIFFRACTION100
1.83-1.890.18362080.13293733X-RAY DIFFRACTION100
1.89-1.950.1741820.13753796X-RAY DIFFRACTION100
1.95-2.020.1882140.13263725X-RAY DIFFRACTION100
2.02-2.10.16861970.1323759X-RAY DIFFRACTION100
2.1-2.190.1972160.13613768X-RAY DIFFRACTION100
2.19-2.310.15271890.13613778X-RAY DIFFRACTION100
2.31-2.450.192060.14383787X-RAY DIFFRACTION100
2.45-2.640.1692140.15113792X-RAY DIFFRACTION100
2.64-2.910.18742100.15833812X-RAY DIFFRACTION100
2.91-3.330.1921900.15383828X-RAY DIFFRACTION100
3.33-4.190.14861890.13843889X-RAY DIFFRACTION100
4.19-47.610.18651970.15294061X-RAY DIFFRACTION100

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