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- PDB-8ze9: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 8ze9
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus S154A mutant in complex with diethylhexyl phthalate at 2.4A
ComponentsTriacylglycerol lipase
KeywordsHYDROLASE / Esterase / Phthalate Ester degrading / ESTS1 / HYDROLASE Diethylhexyl phthalate
Function / homology
Function and homology information


triacylglycerol lipase / hydrolase 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
: / Triacylglycerol lipase
Similarity search - Component
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVerma, S. / Choudhary, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST/TMD-EWO/WTI/2K19/EWFH/2019/8 (G) India
CitationJournal: Structure / Year: 2025
Title: Mechanistic and structural insights into EstS1 esterase: A potent broad-spectrum phthalate diester degrading enzyme.
Authors: Verma, S. / Choudhary, S. / Amith Kumar, K. / Mahto, J.K. / Vamsi K, A.K. / Mishra, I. / Prakash, V.B. / Sircar, D. / Tomar, S. / Kumar Sharma, A. / Singla, J. / Kumar, P.
History
DepositionMay 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triacylglycerol lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2137
Polymers33,3321
Non-polymers8816
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.499, 107.499, 44.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Triacylglycerol lipase


Mass: 33331.953 Da / Num. of mol.: 1 / Mutation: S154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfobacillus acidophilus DSM 10332 (bacteria)
Gene: Sulac_0033 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G8TV28, triacylglycerol lipase
#2: Chemical ChemComp-TKU / ~{O}1-[(2~{R})-2-ethylhexyl] ~{O}2-[(2~{S})-2-ethylhexyl] benzene-1,2-dicarboxylate / Bis(2-ethylhexyl) phthalate / Diethylhexyl phthalate / 1-O-[(2S)-2-ethylhexyl] 2-O-[(2R)-2-ethylhexyl] benzene-1,2-dicarboxylate


Mass: 390.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.24 Å3/Da / Density % sol: 45.342 % / Description: Rod-shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5 / Details: Lithium sulphate, 0.1M Tris, Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→23.073 Å / Num. obs: 11809 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.337 / Num. unique obs: 11809 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→23.073 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.123 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R: 0.549 / ESU R Free: 0.281 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2464 589 4.995 %
Rwork0.1728 11202 -
all0.176 --
obs-11791 99.772 %
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: 23.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.717 Å20.359 Å20 Å2
2--0.717 Å2-0 Å2
3----2.327 Å2
Refinement stepCycle: LAST / Resolution: 2.4→23.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 60 73 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122428
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6573306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.976521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31210357
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.81510107
X-RAY DIFFRACTIONr_chiral_restr0.1080.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021856
X-RAY DIFFRACTIONr_nbd_refined0.2280.21060
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.23
X-RAY DIFFRACTIONr_mcbond_it1.5382.0951191
X-RAY DIFFRACTIONr_mcangle_it2.4843.1261485
X-RAY DIFFRACTIONr_scbond_it2.532.5111237
X-RAY DIFFRACTIONr_scangle_it3.9083.6081819
X-RAY DIFFRACTIONr_lrange_it7.33734.6793527
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.292430.1998250.2048680.9460.9731000.183
2.462-2.5280.237370.1847910.1878280.9570.9771000.169
2.528-2.6010.2350.1837640.1847990.9720.9781000.162
2.601-2.680.296430.1857460.197890.9520.9781000.167
2.68-2.7660.349320.2027400.2087730.9230.97299.87060.18
2.766-2.8620.277410.1936970.1987380.9540.9751000.174
2.862-2.9680.27460.1866800.1927260.9530.9761000.17
2.968-3.0870.247190.1776640.1796830.9620.9791000.163
3.087-3.2220.258370.1866270.1916640.960.9771000.172
3.222-3.3760.307270.1836070.1896340.9450.9781000.171
3.376-3.5540.211220.1745870.1756090.9780.9811000.164
3.554-3.7640.213480.1525300.1575790.970.98599.82730.144
3.764-4.0170.203180.1695280.175460.9710.9821000.16
4.017-4.3270.23270.1474760.1515040.9730.98899.80160.144
4.327-4.7240.269190.1394430.1434620.9650.991000.138
4.724-5.2540.197250.1554050.1584300.980.9841000.154
5.254-6.0150.206190.1763710.1773920.9810.98699.48980.171
6.015-7.2450.221200.1613090.1643320.9740.98599.09640.156
7.245-9.7750.303130.1442490.152650.9710.98898.86790.145
9.775-23.0730.222180.2021630.2041810.9690.9731000.203

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