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- PDB-9j5c: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 9j5c
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with diethylhexyl phthalate
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / ESTS1 / phthalate ester degrading esterase / 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: 2.7 Å
AuthorsVerma, 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
DepositionAug 11, 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: Alpha/beta hydrolase fold-3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9583
Polymers34,1771
Non-polymers7812
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.258, 108.258, 44.872
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 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
Source: (gene. exp.) Sulfobacillus acidophilus DSM 10332 (bacteria)
Gene: Sulac_0033 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8TV28
#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.: 2 / Source method: obtained synthetically / Formula: C24H38O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.278 Å3/Da / Density % sol: 46.049 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7
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: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→25.64 Å / Num. obs: 8440 / % possible obs: 99.9 % / Redundancy: 3.06 % / Rrim(I) all: 0.43 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 8440 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→23.45 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.75 / SU B: 41.144 / SU ML: 0.384 / Cross valid method: FREE R-VALUE / ESU R Free: 0.448
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2945 424 5.028 %
Rwork0.214 8009 -
all0.218 --
obs-8433 99.834 %
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: 5 Å2
Baniso -1Baniso -2Baniso -3
1-0.405 Å20.202 Å20 Å2
2--0.405 Å2-0 Å2
3----1.313 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 56 84 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122441
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162237
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.6653331
X-RAY DIFFRACTIONr_angle_other_deg0.3691.5635218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.299523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42910361
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.91210110
X-RAY DIFFRACTIONr_chiral_restr0.0520.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022803
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
X-RAY DIFFRACTIONr_nbd_refined0.2160.2521
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22303
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21171
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21200
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.215
X-RAY DIFFRACTIONr_nbd_other0.1840.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.26
X-RAY DIFFRACTIONr_mcbond_it00.051192
X-RAY DIFFRACTIONr_mcbond_other00.051192
X-RAY DIFFRACTIONr_mcangle_it00.0751489
X-RAY DIFFRACTIONr_mcangle_other00.0751490
X-RAY DIFFRACTIONr_scbond_it00.051249
X-RAY DIFFRACTIONr_scbond_other00.051250
X-RAY DIFFRACTIONr_scangle_it00.0751837
X-RAY DIFFRACTIONr_scangle_other00.0751838
X-RAY DIFFRACTIONr_lrange_it00.6622694
X-RAY DIFFRACTIONr_lrange_other00.6592684
X-RAY DIFFRACTIONr_rigid_bond_restr0.01234678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7690.45350.263575X-RAY DIFFRACTION100
2.769-2.8440.389260.225572X-RAY DIFFRACTION100
2.844-2.9250.241320.21557X-RAY DIFFRACTION100
2.925-3.0140.281370.194511X-RAY DIFFRACTION100
3.014-3.1110.331250.202505X-RAY DIFFRACTION100
3.111-3.2180.284260.214515X-RAY DIFFRACTION100
3.218-3.3370.202250.2488X-RAY DIFFRACTION100
3.337-3.4710.22240.211461X-RAY DIFFRACTION100
3.471-3.6210.31230.225450X-RAY DIFFRACTION100
3.621-3.7930.264320.239431X-RAY DIFFRACTION100
3.793-3.9930.248160.22410X-RAY DIFFRACTION100
3.993-4.2270.291210.181389X-RAY DIFFRACTION100
4.227-4.5090.293150.181387X-RAY DIFFRACTION100
4.509-4.8550.19690.157343X-RAY DIFFRACTION100
4.855-5.2960.386170.194316X-RAY DIFFRACTION100
5.296-5.8840.385130.218302X-RAY DIFFRACTION100
5.884-6.7240.413110.215263X-RAY DIFFRACTION100
6.724-80.253180.177218X-RAY DIFFRACTION100
8-8.0710.177150.177186X-RAY DIFFRACTION100
8.071-100.20140.201129X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -26.3822 Å / Origin y: -30.2149 Å / Origin z: -0.3103 Å
111213212223313233
T0.0283 Å20.0132 Å2-0.0042 Å2-0.0283 Å2-0.0007 Å2--0.0057 Å2
L1.3907 °2-0.3432 °20.1812 °2-1.6396 °20.1342 °2--1.9836 °2
S0.024 Å °0.0847 Å °0.059 Å °-0.0456 Å °-0.0436 Å °0.0287 Å °-0.083 Å °0.142 Å °0.0197 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 304
2X-RAY DIFFRACTION1A401 - 402

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