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- PDB-9d1k: The alpha-E7 carboxylesterase from Anopheles gambiae -

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Basic information

Entry
Database: PDB / ID: 9d1k
TitleThe alpha-E7 carboxylesterase from Anopheles gambiae
Components(Carboxylic ester ...) x 4
KeywordsHYDROLASE / insect esterase / carboxylesterase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity
Similarity search - Function
Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsFrkic, R.L. / Esmaeily, M. / 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: The alpha-E7 carboxylesterase from Anopheles gambiae
Authors: Frkic, R.L. / Esmaeily, M. / 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
B: Carboxylic ester hydrolase
C: Carboxylic ester hydrolase
D: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,16219
Polymers240,8454
Non-polymers2,31715
Water17,222956
1
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1349
Polymers60,1951
Non-polymers9398
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9735
Polymers60,2211
Non-polymers7524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4902
Polymers60,2081
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5653
Polymers60,2211
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.517, 108.119, 115.623
Angle α, β, γ (deg.)90.00, 101.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Carboxylic ester ... , 4 types, 4 molecules ABCD

#1: Protein Carboxylic ester hydrolase


Mass: 60194.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: 1276889, AgaP_AGAP006228 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7PPB0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Protein Carboxylic ester hydrolase


Mass: 60220.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: 1276889, AgaP_AGAP006228 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7PPB0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#3: Protein Carboxylic ester hydrolase


Mass: 60207.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: 1276889, AgaP_AGAP006228 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7PPB0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#4: Protein Carboxylic ester hydrolase


Mass: 60220.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: 1276889, AgaP_AGAP006228 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7PPB0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Non-polymers , 10 types, 971 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#10: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#11: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#12: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#13: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 24% PEG 4K, 0.2M MgCl2, 0.1M Tris pH 8.1

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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 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.79→48.79 Å / Num. obs: 197265 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.035 / Rrim(I) all: 0.071 / Χ2: 1.06 / Net I/σ(I): 10.9 / Num. measured all: 787182
Reflection shellResolution: 1.79→1.82 Å / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 1.434 / Num. measured all: 40613 / Num. unique obs: 9791 / CC1/2: 0.368 / Rpim(I) all: 0.807 / Rrim(I) all: 1.65 / Χ2: 1.07 / 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: 1.79→48.79 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 9898 5.02 %
Rwork0.2067 --
obs0.2085 197116 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16850 0 153 956 17959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.888
X-RAY DIFFRACTIONf_dihedral_angle_d16.4846450
X-RAY DIFFRACTIONf_chiral_restr0.0542565
X-RAY DIFFRACTIONf_plane_restr0.0073111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.39183550.3636197X-RAY DIFFRACTION100
1.81-1.830.40593310.35446229X-RAY DIFFRACTION100
1.83-1.850.36973030.32326251X-RAY DIFFRACTION100
1.85-1.880.35353340.32516239X-RAY DIFFRACTION100
1.88-1.90.34883430.30866292X-RAY DIFFRACTION100
1.9-1.930.34843210.32416232X-RAY DIFFRACTION99
1.93-1.960.34173240.29546212X-RAY DIFFRACTION100
1.96-1.980.34863290.27866211X-RAY DIFFRACTION100
1.98-2.020.2933370.26886263X-RAY DIFFRACTION100
2.02-2.050.33273340.27946243X-RAY DIFFRACTION100
2.05-2.080.3283430.28486249X-RAY DIFFRACTION100
2.08-2.120.30563400.26946233X-RAY DIFFRACTION100
2.12-2.160.28373600.25026223X-RAY DIFFRACTION100
2.16-2.210.28593470.24746257X-RAY DIFFRACTION100
2.21-2.260.31813170.25266247X-RAY DIFFRACTION99
2.26-2.310.28273080.24356250X-RAY DIFFRACTION100
2.31-2.370.28463320.24026286X-RAY DIFFRACTION100
2.37-2.430.28033230.22876257X-RAY DIFFRACTION100
2.43-2.50.27323480.22586245X-RAY DIFFRACTION100
2.5-2.580.26623210.21846271X-RAY DIFFRACTION100
2.58-2.670.27693210.21816275X-RAY DIFFRACTION100
2.67-2.780.27213210.22616288X-RAY DIFFRACTION100
2.78-2.910.29543410.23176233X-RAY DIFFRACTION100
2.91-3.060.24133240.22086240X-RAY DIFFRACTION100
3.06-3.250.26193280.21526250X-RAY DIFFRACTION99
3.25-3.50.26323100.20286222X-RAY DIFFRACTION98
3.5-3.860.21233210.17696139X-RAY DIFFRACTION97
3.86-4.410.17223130.15766130X-RAY DIFFRACTION97
4.41-5.560.17382910.14856254X-RAY DIFFRACTION98
5.56-48.790.16283780.14776300X-RAY DIFFRACTION98

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