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- PDB-9d1q: Lucilia cuprina alpha esterase 7 directed evolution round 6 -

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Basic information

Entry
Database: PDB / ID: 9d1q
TitleLucilia cuprina alpha esterase 7 directed evolution round 6
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: 1.35 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 6
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)66,5708
Polymers65,9241
Non-polymers6477
Water11,385632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.104, 92.236, 105.774
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: 65923.641 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.: 3 / 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.: 632 / 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: 42.78 %
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→45.88 Å / Num. obs: 125243 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Rrim(I) all: 0.12 / Χ2: 0.94 / Net I/σ(I): 11.1 / Num. measured all: 1557959
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 2.707 / Num. measured all: 76495 / Num. unique obs: 6108 / CC1/2: 0.49 / Rpim(I) all: 0.8 / Rrim(I) all: 2.825 / Χ2: 0.74 / 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→45.88 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 6229 4.98 %
Rwork0.1717 --
obs0.1729 125083 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 43 632 5263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.944
X-RAY DIFFRACTIONf_dihedral_angle_d11.66765
X-RAY DIFFRACTIONf_chiral_restr0.082705
X-RAY DIFFRACTIONf_plane_restr0.008862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.292220.30783880X-RAY DIFFRACTION100
1.37-1.380.31352280.29693903X-RAY DIFFRACTION100
1.38-1.40.28721740.27673952X-RAY DIFFRACTION100
1.4-1.420.28822100.26823940X-RAY DIFFRACTION100
1.42-1.430.25341790.25043914X-RAY DIFFRACTION100
1.43-1.450.27812160.25553944X-RAY DIFFRACTION100
1.45-1.480.27542100.24293889X-RAY DIFFRACTION100
1.48-1.50.26362140.23813901X-RAY DIFFRACTION100
1.5-1.520.26221980.23643941X-RAY DIFFRACTION100
1.52-1.550.26692050.23033929X-RAY DIFFRACTION100
1.55-1.570.21562010.2123947X-RAY DIFFRACTION100
1.57-1.60.22241990.19733912X-RAY DIFFRACTION100
1.6-1.630.23361980.1933964X-RAY DIFFRACTION100
1.63-1.660.19172190.17373895X-RAY DIFFRACTION100
1.66-1.70.19752080.17593967X-RAY DIFFRACTION100
1.7-1.740.19232120.17253908X-RAY DIFFRACTION100
1.74-1.780.20582010.16993949X-RAY DIFFRACTION100
1.78-1.830.19692240.1793959X-RAY DIFFRACTION100
1.83-1.890.20482260.18393928X-RAY DIFFRACTION100
1.89-1.950.2081840.18553982X-RAY DIFFRACTION100
1.95-2.020.21592180.17163934X-RAY DIFFRACTION100
2.02-2.10.20281950.17723984X-RAY DIFFRACTION100
2.1-2.190.19522100.16553971X-RAY DIFFRACTION100
2.19-2.310.17732340.1633959X-RAY DIFFRACTION100
2.31-2.450.17112180.16473966X-RAY DIFFRACTION100
2.45-2.640.21292130.1694015X-RAY DIFFRACTION100
2.64-2.910.18441980.17484017X-RAY DIFFRACTION100
2.91-3.330.19872060.15984029X-RAY DIFFRACTION100
3.33-4.190.16161990.14044115X-RAY DIFFRACTION100
4.19-45.880.1822100.14964260X-RAY DIFFRACTION100

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