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- PDB-9j1g: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 9j1g
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with phthalate
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / ESTS1 / phthalate ester degrading esterase / Sulfobacillus acidophilus / 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
PHTHALIC 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 5, 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)35,06812
Polymers34,1771
Non-polymers89111
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.386, 108.386, 44.628
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-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.27 Å3/Da / Density % sol: 45.88 % / Description: Rod shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Sodium malonate, 0.1 M HEPES (pH 7.0), and 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 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→27.12 Å / Num. obs: 48160 / % possible obs: 99.2 % / Redundancy: 2.87 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 15.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.375 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 48160 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→27.111 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.971 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1627 2385 4.954 %
Rwork0.1179 45759 -
all0.12 --
obs-48144 99.961 %
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: 14.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.531 Å2-0.265 Å2-0 Å2
2---0.531 Å20 Å2
3---1.721 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 60 315 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122470
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162253
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.6733365
X-RAY DIFFRACTIONr_angle_other_deg0.5251.5625253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.961520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98810371
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.51610112
X-RAY DIFFRACTIONr_chiral_restr0.0830.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
X-RAY DIFFRACTIONr_nbd_refined0.2280.2494
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22079
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21190
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2217
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.213
X-RAY DIFFRACTIONr_nbd_other0.1740.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.227
X-RAY DIFFRACTIONr_mcbond_it2.2281.1621204
X-RAY DIFFRACTIONr_mcbond_other2.2281.1611204
X-RAY DIFFRACTIONr_mcangle_it2.8861.7511506
X-RAY DIFFRACTIONr_mcangle_other2.9121.7541507
X-RAY DIFFRACTIONr_scbond_it4.8081.7071266
X-RAY DIFFRACTIONr_scbond_other4.8111.7091267
X-RAY DIFFRACTIONr_scangle_it5.252.3481850
X-RAY DIFFRACTIONr_scangle_other5.2492.3491851
X-RAY DIFFRACTIONr_lrange_it6.12125.7592845
X-RAY DIFFRACTIONr_lrange_other5.38221.7172739
X-RAY DIFFRACTIONr_rigid_bond_restr7.19734723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2311890.2083366X-RAY DIFFRACTION99.8315
1.539-1.5810.2431640.183259X-RAY DIFFRACTION100
1.581-1.6270.2251720.1613154X-RAY DIFFRACTION100
1.627-1.6760.1811630.1413112X-RAY DIFFRACTION100
1.676-1.7310.1851600.1272963X-RAY DIFFRACTION100
1.731-1.7920.1671690.1192877X-RAY DIFFRACTION100
1.792-1.8590.211550.1222825X-RAY DIFFRACTION100
1.859-1.9350.1591310.0972701X-RAY DIFFRACTION100
1.935-2.020.1671580.0992561X-RAY DIFFRACTION100
2.02-2.1180.1491310.12469X-RAY DIFFRACTION100
2.118-2.2320.1471180.0912380X-RAY DIFFRACTION100
2.232-2.3660.1481050.0892224X-RAY DIFFRACTION100
2.366-2.5280.131970.0962113X-RAY DIFFRACTION100
2.528-2.7290.16910.0961993X-RAY DIFFRACTION100
2.729-2.9860.144830.1091834X-RAY DIFFRACTION100
2.986-3.3340.136770.1171647X-RAY DIFFRACTION100
3.334-3.840.155660.1191463X-RAY DIFFRACTION100
3.84-4.680.107510.1071269X-RAY DIFFRACTION100
4.68-6.5220.188540.14981X-RAY DIFFRACTION100
6.522-100.158510.158568X-RAY DIFFRACTION99.6779

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