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- PDB-9g73: Crystal structure of mouse Carboxylesterase 2e (Ces2e) -

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Basic information

Entry
Database: PDB / ID: 9g73
TitleCrystal structure of mouse Carboxylesterase 2e (Ces2e)
ComponentsPyrethroid hydrolase Ces2e
KeywordsHYDROLASE / carboxylesterase 2e / protein structure / lipid metabolism / X-ray crystallography / alpha/beta-hydrolase fold / biochemistry / lipid hydrolysis / non-alcoholic fatty liver disease
Function / homology
Function and homology information


pyrethroid hydrolase / trans-permethrin hydrolase activity / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / carboxylesterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / endoplasmic reticulum
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Pyrethroid hydrolase Ces2e
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEisner, H. / Sagmeister, T. / Rammer, L. / Oberer, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundDOI: 10.55776/F73 Austria
Austrian Science FundDOI: 10.55776/DOC50 Austria
CitationJournal: To Be Published
Title: Crystal structure of mouse Ces2e
Authors: Eisner, H. / Rammer, L. / Riegler-Berket, L. / Rodriguez Gamez, C. / Sagmeister, T. / Chalhoub, G. / Liesinger, L. / Birner-Gruenberger, R. / Pavkov-Keller, T. / Haemmerle, G. / Schoiswohl, G. / Oberer, M.
History
DepositionJul 19, 2024Deposition site: PDBE / Processing site: PDBE
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: Pyrethroid hydrolase Ces2e
B: Pyrethroid hydrolase Ces2e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,53023
Polymers126,4272
Non-polymers4,10321
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-164 kcal/mol
Surface area43490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.931, 145.243, 149.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 28 - 550 / Label seq-ID: 28 - 550

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyrethroid hydrolase Ces2e / Carboxylic ester hydrolase / carboxylesterase 2E


Mass: 63213.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ces2e, Ces5 / Cell line (production host): HEK / Production host: Homo sapiens (human)
References: UniProt: Q8BK48, pyrethroid hydrolase, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 717 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Protein stock solution in 20 mM Tris/HCl, pH 7.4, and 150 mM NaCl; ShotGun (SG1) Screen: E1 (2.0 M ammonium sulfate and 0.1 M Bis-Tris buffer pH 5.5) with protein end concentration of 2.89 mg/ml in a 0.5 uL drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.4→80.646 Å / Num. obs: 54113 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.0755 / Net I/σ(I): 9.38
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.4157 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 5365 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→80.646 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.997 / SU ML: 0.176 / Cross valid method: FREE R-VALUE / ESU R: 0.337 / ESU R Free: 0.22
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2138 2718 5.023 %
Rwork0.1756 51393 -
all0.178 --
obs-54111 99.856 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.312 Å2
Baniso -1Baniso -2Baniso -3
1--1.461 Å2-0 Å20 Å2
2---1.111 Å2-0 Å2
3---2.572 Å2
Refinement stepCycle: LAST / Resolution: 2.4→80.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8154 0 249 698 9101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157983
X-RAY DIFFRACTIONr_ext_dist_refined_d0.2810.136478
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.66511803
X-RAY DIFFRACTIONr_angle_other_deg1.3011.59718474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04151047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21322.922421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.344151385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2111540
X-RAY DIFFRACTIONr_chiral_restr0.0780.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021900
X-RAY DIFFRACTIONr_nbd_refined0.1940.21681
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.27345
X-RAY DIFFRACTIONr_nbtor_refined0.160.24105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.23778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2491
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.239
X-RAY DIFFRACTIONr_nbd_other0.220.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.214
X-RAY DIFFRACTIONr_mcbond_it3.0183.454183
X-RAY DIFFRACTIONr_mcbond_other3.0073.4494182
X-RAY DIFFRACTIONr_mcangle_it4.8755.1595230
X-RAY DIFFRACTIONr_mcangle_other4.8755.165231
X-RAY DIFFRACTIONr_scbond_it4.1344.1764497
X-RAY DIFFRACTIONr_scbond_other4.134.1554438
X-RAY DIFFRACTIONr_scangle_it6.4996.0266570
X-RAY DIFFRACTIONr_scangle_other6.5045.9916481
X-RAY DIFFRACTIONr_lrange_it10.30971.6440964
X-RAY DIFFRACTIONr_lrange_other10.22871.64840423
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.0517193
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.09360.05009
12BX-RAY DIFFRACTIONLocal ncs0.09360.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.281790.2533789X-RAY DIFFRACTION99.9748
2.462-2.530.2782230.2423622X-RAY DIFFRACTION99.974
2.53-2.6030.2791960.2413591X-RAY DIFFRACTION100
2.603-2.6830.2521610.2253482X-RAY DIFFRACTION100
2.683-2.7710.2251570.2123384X-RAY DIFFRACTION100
2.771-2.8680.2491690.2123265X-RAY DIFFRACTION100
2.868-2.9760.2471850.1963113X-RAY DIFFRACTION100
2.976-3.0980.2441700.1763031X-RAY DIFFRACTION99.9688
3.098-3.2350.2131510.1682925X-RAY DIFFRACTION100
3.235-3.3930.2091370.1582781X-RAY DIFFRACTION99.9315
3.393-3.5760.2121410.1572668X-RAY DIFFRACTION99.8933
3.576-3.7930.1851470.142484X-RAY DIFFRACTION99.962
3.793-4.0540.1471070.1332402X-RAY DIFFRACTION100
4.054-4.3790.191310.1332199X-RAY DIFFRACTION99.9571
4.379-4.7950.1611090.132040X-RAY DIFFRACTION99.907
4.795-5.360.1981030.1521852X-RAY DIFFRACTION99.6432
5.36-6.1860.205860.1891632X-RAY DIFFRACTION99.8837
6.186-7.5680.225780.2041411X-RAY DIFFRACTION99.9329
7.568-10.6690.15550.1491116X-RAY DIFFRACTION99.7445

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