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- PDB-9wnz: EstS1 esterase in complex with mono(2-hydroxyethyl) terephthalate... -

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Basic information

Entry
Database: PDB / ID: 9wnz
TitleEstS1 esterase in complex with mono(2-hydroxyethyl) terephthalate (MHET) and Bis(2-hydroxyethyl) terephthalate (BHET)
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / EstS1 esterase / mono(2-hydroxyethyl) terephthalate (MHET) / Bis(2-hydroxyethyl) terephthalate (BHET)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity
Similarity search - Function
Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
bis(2-hydroxyethyl) benzene-1,4-dicarboxylate / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / IMIDAZOLE / Triacylglycerol lipase
Similarity search - Component
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVerma, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR45880/BCE/8/1634/2022 India
CitationJournal: J.Struct.Biol. / Year: 2026
Title: Structural and functional characterization of thermostable EstS1 esterase for BHET degradation.
Authors: Verma, S. / Aggarwal, D. / Ashar, M. / Pandey, A.K. / Sutradhar, A. / Pandey, S. / Sircar, D. / Singla, J. / Kumar, P.
History
DepositionSep 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold-3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7725
Polymers34,1771
Non-polymers5964
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint5 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.748, 106.748, 44.95
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha/beta hydrolase fold-3 domain-containing protein / ESTS1 phthalate ester degradaring esterase


Mass: 34176.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EstS1 esterase in complex with mono(2-hydroxyethyl) terephthalate (MHET) and Bis(2-hydroxyethyl) terephthalate (BHET)
Source: (gene. exp.) Sulfobacillus acidophilus DSM 10332 (bacteria)
Gene: Sulac_0033 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8TV28

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-C8X / bis(2-hydroxyethyl) benzene-1,4-dicarboxylate / bis(2-hydroxyethyl) terephthalate


Mass: 254.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.21917367 Å3/Da / Density % sol: 44.6 % / Description: Rod shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7
Details: 100 mM HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001, and 1.1 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→27.59 Å / Num. obs: 15070 / % possible obs: 99.9 % / Redundancy: 8.063 % / CC1/2: 0.995 / Net I/σ(I): 18.2
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 8.9 / Num. unique obs: 1304 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.2→21.848 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.848 / SU B: 7.301 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / ESU R: 0.339 / ESU R Free: 0.238 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2532 770 5.113 %
Rwork0.1969 14289 -
all0.2 --
obs-15059 99.861 %
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: 12.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.568 Å20.284 Å20 Å2
2--0.568 Å2-0 Å2
3----1.842 Å2
Refinement stepCycle: LAST / Resolution: 2.2→21.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 42 62 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122520
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.8283445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.384530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66510381
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.82810114
X-RAY DIFFRACTIONr_chiral_restr0.1410.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022025
X-RAY DIFFRACTIONr_nbd_refined0.2370.21231
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2930.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.212
X-RAY DIFFRACTIONr_mcbond_it1.2281.0751245
X-RAY DIFFRACTIONr_mcangle_it2.0381.921572
X-RAY DIFFRACTIONr_scbond_it1.7791.3311275
X-RAY DIFFRACTIONr_scangle_it2.7612.331873
X-RAY DIFFRACTIONr_lrange_it5.60113.0953862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.321570.2431031X-RAY DIFFRACTION100
2.257-2.3180.323510.2261032X-RAY DIFFRACTION100
2.318-2.3840.317400.212984X-RAY DIFFRACTION100
2.384-2.4570.313320.223977X-RAY DIFFRACTION100
2.457-2.5360.271610.225926X-RAY DIFFRACTION100
2.536-2.6240.27500.222892X-RAY DIFFRACTION100
2.624-2.7210.304440.216868X-RAY DIFFRACTION100
2.721-2.8310.306390.218848X-RAY DIFFRACTION100
2.831-2.9540.306550.214793X-RAY DIFFRACTION100
2.954-3.0960.283280.201770X-RAY DIFFRACTION99.8748
3.096-3.260.222510.191729X-RAY DIFFRACTION100
3.26-3.4530.214400.178707X-RAY DIFFRACTION100
3.453-3.6840.294410.162645X-RAY DIFFRACTION99.8544
3.684-3.970.177470.162601X-RAY DIFFRACTION100
3.97-4.3350.207360.154553X-RAY DIFFRACTION100
4.335-4.8230.236250.157536X-RAY DIFFRACTION100
4.823-5.5240.196180.18467X-RAY DIFFRACTION100
5.524-6.660.222260.198396X-RAY DIFFRACTION100
6.66-9.0090.126190.169321X-RAY DIFFRACTION100
8-100.162100.162213X-RAY DIFFRACTION100

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