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- PDB-9j1e: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 9j1e
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus at 1.22A
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / ESTS1 / phthalate ester degrading esterase / Sulfobacillus acidophilus
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
ACETYL GROUP / MALONATE ION / Triacylglycerol lipase
Similarity search - Component
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.22 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 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: Alpha/beta hydrolase fold-3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,88212
Polymers34,1771
Non-polymers70511
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.710, 107.710, 44.402
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.231794 Å3/Da / Density % sol: 44.92 % / Description: Rod shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Sodium malonate, 0.1 M HEPES (pH 7.0), 0.5% 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: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.22→27.61 Å / Num. obs: 1117439 / % possible obs: 100 % / Redundancy: 3.26 % / Rrim(I) all: 0.132 / Net I/σ(I): 15.5
Reflection shellResolution: 1.22→1.24 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 91912 / 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: 1.22→25.884 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.52 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2037 4733 5.151 %
Rwork0.173 87159 -
all0.175 --
obs-91892 99.96 %
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: 13.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.584 Å2-0.292 Å2-0 Å2
2---0.584 Å20 Å2
3---1.895 Å2
Refinement stepCycle: LAST / Resolution: 1.22→25.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 46 232 2581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122521
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162308
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6633443
X-RAY DIFFRACTIONr_angle_other_deg0.5741.5585400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.602521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28610388
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0610117
X-RAY DIFFRACTIONr_chiral_restr0.090.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined0.230.2510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22145
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21210
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2153
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.214
X-RAY DIFFRACTIONr_nbd_other0.1860.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.225
X-RAY DIFFRACTIONr_mcbond_it2.1991.1661228
X-RAY DIFFRACTIONr_mcbond_other2.1991.1661229
X-RAY DIFFRACTIONr_mcangle_it2.4821.7541539
X-RAY DIFFRACTIONr_mcangle_other2.4821.7551540
X-RAY DIFFRACTIONr_scbond_it6.5571.6241293
X-RAY DIFFRACTIONr_scbond_other6.5541.6251294
X-RAY DIFFRACTIONr_scangle_it5.9582.2681888
X-RAY DIFFRACTIONr_scangle_other5.9572.2691889
X-RAY DIFFRACTIONr_lrange_it4.96322.0752829
X-RAY DIFFRACTIONr_lrange_other4.77519.2522774
X-RAY DIFFRACTIONr_rigid_bond_restr17.80734829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.2310.3473320.3476345X-RAY DIFFRACTION99.6716
1.231-1.2650.3363460.3346265X-RAY DIFFRACTION100
1.265-1.3010.3293350.3116049X-RAY DIFFRACTION100
1.301-1.3410.2993450.2945918X-RAY DIFFRACTION100
1.341-1.3850.2813150.2635686X-RAY DIFFRACTION100
1.385-1.4340.292670.2535573X-RAY DIFFRACTION100
1.434-1.4880.2672730.2165346X-RAY DIFFRACTION100
1.488-1.5480.2412730.1945154X-RAY DIFFRACTION100
1.548-1.6170.2262650.174933X-RAY DIFFRACTION100
1.617-1.6950.1842610.1464750X-RAY DIFFRACTION100
1.695-1.7870.1962440.1394488X-RAY DIFFRACTION100
1.787-1.8940.1742540.1394243X-RAY DIFFRACTION100
1.894-2.0240.1772230.134015X-RAY DIFFRACTION100
2.024-2.1850.1652130.1223714X-RAY DIFFRACTION100
2.185-2.3920.1381830.1123457X-RAY DIFFRACTION99.9725
2.392-2.6720.1471840.1233106X-RAY DIFFRACTION100
2.672-3.080.1771410.1372790X-RAY DIFFRACTION99.9659
3.08-3.7590.1881240.1452377X-RAY DIFFRACTION100
3.759-5.260.1491140.1291831X-RAY DIFFRACTION99.9486
5.26-100.168410.1621118X-RAY DIFFRACTION99.9138

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