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- PDB-9j58: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 9j58
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with jeffamine
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / ESTS1 / phthalate ester degrading esterase / Sulfobacillus acidophilus / jeffamine
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
Chem-JEF / MALONIC ACID / Triacylglycerol lipase
Similarity search - Component
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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)35,60314
Polymers34,1771
Non-polymers1,42713
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.078, 108.078, 44.510
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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.25 Å3/Da / Density % sol: 45.42 % / Description: ROD SHAPED
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: Aug 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→27.69 Å / Num. obs: 47748 / % possible obs: 100 % / Redundancy: 2.95 % / Rrim(I) all: 0.05 / Net I/σ(I): 27
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 47748 / Rrim(I) all: 0.655 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrysalisProdata reduction
CrysalisProdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→25.973 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.477 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1633 2361 4.946 %
Rwork0.117 45372 -
all0.119 --
obs-47733 99.964 %
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: 16.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.505 Å20.253 Å20 Å2
2--0.505 Å2-0 Å2
3----1.638 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 82 218 2602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122488
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162289
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6693380
X-RAY DIFFRACTIONr_angle_other_deg0.5131.5575334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.761520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18510365
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.09810111
X-RAY DIFFRACTIONr_chiral_restr0.0780.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_nbd_refined0.2310.2451
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22111
X-RAY DIFFRACTIONr_nbtor_refined0.180.21190
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.211
X-RAY DIFFRACTIONr_nbd_other0.1770.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.218
X-RAY DIFFRACTIONr_mcbond_it2.5091.3091208
X-RAY DIFFRACTIONr_mcbond_other2.5091.3141209
X-RAY DIFFRACTIONr_mcangle_it3.0251.9621510
X-RAY DIFFRACTIONr_mcangle_other3.031.9681511
X-RAY DIFFRACTIONr_scbond_it5.9661.9591280
X-RAY DIFFRACTIONr_scbond_other5.9641.9591281
X-RAY DIFFRACTIONr_scangle_it6.1572.6821864
X-RAY DIFFRACTIONr_scangle_other6.1552.6821865
X-RAY DIFFRACTIONr_lrange_it5.00721.7132707
X-RAY DIFFRACTIONr_lrange_other521.6832706
X-RAY DIFFRACTIONr_rigid_bond_restr6.60734775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.1931840.1553336X-RAY DIFFRACTION99.8865
1.539-1.5810.2291640.1413213X-RAY DIFFRACTION100
1.581-1.6270.1831600.1253156X-RAY DIFFRACTION100
1.627-1.6760.1751700.1133022X-RAY DIFFRACTION100
1.676-1.7310.1651530.1042991X-RAY DIFFRACTION100
1.731-1.7920.1721750.1042852X-RAY DIFFRACTION100
1.792-1.8590.1971510.1082789X-RAY DIFFRACTION100
1.859-1.9340.161360.1062667X-RAY DIFFRACTION100
1.934-2.020.1771480.1042560X-RAY DIFFRACTION100
2.02-2.1180.1631340.1042462X-RAY DIFFRACTION100
2.118-2.2320.1561160.1082330X-RAY DIFFRACTION100
2.232-2.3660.1581020.12224X-RAY DIFFRACTION100
2.366-2.5280.1291010.1022102X-RAY DIFFRACTION100
2.528-2.7280.185850.1111960X-RAY DIFFRACTION100
2.728-2.9850.151830.121814X-RAY DIFFRACTION100
2.985-3.3320.152850.1311636X-RAY DIFFRACTION100
3.332-3.8370.139600.1271458X-RAY DIFFRACTION100
3.837-4.6740.103490.1021260X-RAY DIFFRACTION100
4.674-6.5050.19540.153972X-RAY DIFFRACTION100
6.505-100.175510.162567X-RAY DIFFRACTION99.6774

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