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- PDB-9wny: EstS1 esterase active site mutant S154A in complex with Bis(2-hyd... -

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Basic information

Entry
Database: PDB / ID: 9wny
TitleEstS1 esterase active site mutant S154A in complex with Bis(2-hydroxyethyl) terephthalate (BHET)
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / EstS1 esterase / Bis(2-hydroxyethyl) terephthalate (BHET) / PET degradation
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 / Triacylglycerol lipase
Similarity search - Component
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 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)34,6693
Polymers34,1611
Non-polymers5082
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.502, 106.502, 44.945
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 34160.836 Da / Num. of mol.: 1 / Mutation: S154A
Source method: isolated from a genetically manipulated source
Details: EstS1 esterase active site mutant S154A
Source: (gene. exp.) Sulfobacillus acidophilus DSM 10332 (bacteria)
Gene: Sulac_0033 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8TV28
#2: Chemical ChemComp-C8X / bis(2-hydroxyethyl) benzene-1,4-dicarboxylate / bis(2-hydroxyethyl) terephthalate


Mass: 254.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 2.20869827 Å3/Da / Density % sol: 44.3456879 % / Description: Rod shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001

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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: Jan 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→27.55 Å / Num. obs: 19907 / % possible obs: 100 % / Redundancy: 15.04 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.037 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1466 / CC1/2: 0.925 / % possible all: 100

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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→22.482 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 3.905 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.164 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2232 1008 5.068 %
Rwork0.1786 18882 -
all0.181 --
obs-19890 99.91 %
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: 12.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.077 Å20.039 Å2-0 Å2
2--0.077 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2→22.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 36 95 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122430
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.8253324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.494528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31710366
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.16810108
X-RAY DIFFRACTIONr_chiral_restr0.120.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021920
X-RAY DIFFRACTIONr_nbd_refined0.2360.21206
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2126
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.216
X-RAY DIFFRACTIONr_mcbond_it1.2341.011194
X-RAY DIFFRACTIONr_mcangle_it2.0271.8071493
X-RAY DIFFRACTIONr_scbond_it2.2471.3981236
X-RAY DIFFRACTIONr_scangle_it3.5492.41823
X-RAY DIFFRACTIONr_lrange_it6.01913.1293788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.224940.191362X-RAY DIFFRACTION100
2.052-2.1070.256750.1931323X-RAY DIFFRACTION100
2.107-2.1680.219640.2021308X-RAY DIFFRACTION100
2.168-2.2340.238460.1931286X-RAY DIFFRACTION100
2.234-2.3060.273680.2071234X-RAY DIFFRACTION100
2.306-2.3870.183430.181214X-RAY DIFFRACTION100
2.387-2.4760.297680.1821141X-RAY DIFFRACTION100
2.476-2.5750.216550.191106X-RAY DIFFRACTION100
2.575-2.6880.232580.1891076X-RAY DIFFRACTION100
2.688-2.8170.225450.1831043X-RAY DIFFRACTION100
2.817-2.9670.236630.186956X-RAY DIFFRACTION100
2.967-3.1440.215440.186906X-RAY DIFFRACTION100
3.144-3.3560.205530.169869X-RAY DIFFRACTION100
3.356-3.6180.207520.158801X-RAY DIFFRACTION100
3.618-3.9540.234470.149751X-RAY DIFFRACTION100
3.954-4.4030.16300.142686X-RAY DIFFRACTION100
4.403-5.0520.148390.141605X-RAY DIFFRACTION100
5.052-6.1110.226220.176528X-RAY DIFFRACTION100
6.111-8.340.221290.183413X-RAY DIFFRACTION100
8-100.34130.179273X-RAY DIFFRACTION99.3056

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