PDB-9d1t: Lucilia cuprina alpha esterase 7 directed evolution round 9

ID or keywords:

Entry

Database: PDB / ID: 9d1t

Title

Lucilia cuprina alpha esterase 7 directed evolution round 9

Components

Carboxylic ester hydrolase

Keywords

HYDROLASE / directed evolution / insecticide resistance

Function / homology

Hydrolases; 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 species

Lucilia cuprina (Australian sheep blowfly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Frkic, R.L. / Fraser, N. / Mabbitt, P.D. / Jackson, C.J.

Funding support

Australia, 2items

Citation

Journal: To Be Published
Title: Lucilia cuprina alpha esterase 7 directed evolution round 9
Authors: Frkic, R.L. / Fraser, N. / Correy, G.J. / Mabbitt, P.D. / Jackson, C.J.

History

Deposition	Aug 7, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9d1t.cif.gz	150.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9d1t.ent.gz	114.6 KB	Display	PDB format
PDBx/mmJSON format	9d1t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9d1t_validation.pdf.gz	463.2 KB	Display	wwPDB validaton report
Full document	9d1t_full_validation.pdf.gz	466 KB	Display
Data in XML	9d1t_validation.xml.gz	33.9 KB	Display
Data in CIF	9d1t_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d1/9d1t ftp://data.pdbj.org/pub/pdb/validation_reports/d1/9d1t	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#54 - Jun 2004 Acetylcholinesterase similarity (4)

Deposited unit

A: Carboxylic ester hydrolase

hetero molecules

67 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	58.147, 92.905, 105.039
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Carboxylic ester hydrolase Mass: 65863.414 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.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.33 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.45→46.45 Å / Num. obs: 101479 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.133 / R_pim(I) all: 0.038 / R_rim(I) all: 0.138 / Χ²: 1.02 / Net I/σ(I): 11.1 / Num. measured all: 1356583
Reflection shell	Resolution: 1.45→1.47 Å / % possible obs: 100 % / Redundancy: 13.6 % / R_merge(I) obs: 2.244 / Num. measured all: 68212 / Num. unique obs: 5010 / CC_1/2: 0.584 / R_pim(I) all: 0.627 / R_rim(I) all: 2.331 / Χ²: 1.03 / Net I/σ(I) obs: 1.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→46.45 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1944	5054	4.99 %
R_work	0.165	-	-
obs	0.1664	101384	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.45→46.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4586	0	76	635	5297

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.878
X-RAY DIFFRACTION	f_dihedral_angle_d	13.482	1852
X-RAY DIFFRACTION	f_chiral_restr	0.078	706
X-RAY DIFFRACTION	f_plane_restr	0.008	854

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.47	0.2903	158	0.2749	3174	X-RAY DIFFRACTION	100
1.47-1.48	0.2579	174	0.2658	3183	X-RAY DIFFRACTION	100
1.48-1.5	0.3255	171	0.2542	3192	X-RAY DIFFRACTION	100
1.5-1.52	0.2711	172	0.2498	3155	X-RAY DIFFRACTION	100
1.52-1.54	0.2495	177	0.2412	3159	X-RAY DIFFRACTION	100
1.54-1.56	0.2949	158	0.2308	3158	X-RAY DIFFRACTION	100
1.56-1.58	0.237	164	0.2184	3205	X-RAY DIFFRACTION	100
1.58-1.61	0.2367	159	0.2074	3166	X-RAY DIFFRACTION	100
1.61-1.63	0.2545	172	0.2051	3183	X-RAY DIFFRACTION	100
1.63-1.66	0.2119	166	0.1857	3190	X-RAY DIFFRACTION	100
1.66-1.69	0.2461	184	0.1855	3179	X-RAY DIFFRACTION	100
1.69-1.72	0.2081	164	0.1734	3174	X-RAY DIFFRACTION	100
1.72-1.75	0.1926	172	0.1692	3189	X-RAY DIFFRACTION	100
1.75-1.79	0.2168	165	0.1668	3182	X-RAY DIFFRACTION	100
1.79-1.83	0.1885	162	0.163	3218	X-RAY DIFFRACTION	100
1.83-1.87	0.2313	162	0.166	3164	X-RAY DIFFRACTION	100
1.87-1.92	0.1886	161	0.1748	3194	X-RAY DIFFRACTION	100
1.92-1.97	0.1784	157	0.1582	3207	X-RAY DIFFRACTION	100
1.97-2.03	0.2246	159	0.1573	3235	X-RAY DIFFRACTION	100
2.03-2.09	0.1882	145	0.16	3233	X-RAY DIFFRACTION	100
2.09-2.17	0.1926	175	0.1623	3188	X-RAY DIFFRACTION	100
2.17-2.25	0.1821	158	0.1562	3220	X-RAY DIFFRACTION	100
2.25-2.36	0.1867	159	0.1569	3217	X-RAY DIFFRACTION	100
2.36-2.48	0.1755	178	0.1597	3221	X-RAY DIFFRACTION	100
2.48-2.63	0.1792	175	0.1592	3242	X-RAY DIFFRACTION	100
2.63-2.84	0.2192	170	0.1674	3232	X-RAY DIFFRACTION	100
2.84-3.12	0.1992	180	0.1651	3240	X-RAY DIFFRACTION	100
3.12-3.58	0.1554	166	0.1483	3293	X-RAY DIFFRACTION	100
3.58-4.5	0.173	179	0.1347	3307	X-RAY DIFFRACTION	100
4.5-46.45	0.1789	212	0.1575	3430	X-RAY DIFFRACTION	100

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