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- PDB-9j59: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 9j59
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / ESTS1 / phthalate ester degrading esterase / Sulfobacillus acidophilus
Function / homologyLipase, 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 / triacylglycerol lipase / Alpha/Beta hydrolase fold / hydrolase activity / Triacylglycerol lipase
Function and homology information
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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)34,6118
Polymers34,1771
Non-polymers4347
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.057, 108.057, 44.542
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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 45.44 %
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: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→25.95 Å / Num. obs: 47747 / % possible obs: 100 % / Redundancy: 2.93 % / Rrim(I) all: 0.171 / Net I/σ(I): 6.5
Reflection shellResolution: 1.55→1.58 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 47747 / Rrim(I) all: 0.817 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.243 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2055 2359 4.943 %
Rwork0.151 45369 -
all0.154 --
obs-47728 99.948 %
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: 15.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.329 Å2-0.165 Å20 Å2
2---0.329 Å20 Å2
3---1.069 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 28 213 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122395
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162189
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6573259
X-RAY DIFFRACTIONr_angle_other_deg0.4931.5575096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.137518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89410354
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.10110107
X-RAY DIFFRACTIONr_chiral_restr0.0750.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined0.2240.2471
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22050
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.216
X-RAY DIFFRACTIONr_nbd_other0.2910.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.50.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_mcbond_it2.4861.3351192
X-RAY DIFFRACTIONr_mcbond_other2.4221.3351192
X-RAY DIFFRACTIONr_mcangle_it3.0462.0021487
X-RAY DIFFRACTIONr_mcangle_other3.0512.0041488
X-RAY DIFFRACTIONr_scbond_it4.4531.8321203
X-RAY DIFFRACTIONr_scbond_other4.4521.8331204
X-RAY DIFFRACTIONr_scangle_it5.2762.5551771
X-RAY DIFFRACTIONr_scangle_other5.2742.5561772
X-RAY DIFFRACTIONr_lrange_it5.30424.1292691
X-RAY DIFFRACTIONr_lrange_other5.22422.662643
X-RAY DIFFRACTIONr_rigid_bond_restr4.88634584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.550.291820.2633332X-RAY DIFFRACTION99.9147
1.56-1.5810.2961640.2383210X-RAY DIFFRACTION100
1.581-1.6270.2791620.2123156X-RAY DIFFRACTION100
1.627-1.6760.2441660.1973033X-RAY DIFFRACTION100
1.676-1.7310.2161520.1782997X-RAY DIFFRACTION100
1.731-1.7920.2371770.1742847X-RAY DIFFRACTION100
1.792-1.8590.2511510.1482782X-RAY DIFFRACTION100
1.859-1.9340.1871370.1342679X-RAY DIFFRACTION100
1.934-2.020.2291480.1362551X-RAY DIFFRACTION100
2.02-2.1180.1981340.1462467X-RAY DIFFRACTION100
2.118-2.2320.2071170.1372330X-RAY DIFFRACTION100
2.232-2.3660.1761010.1272222X-RAY DIFFRACTION100
2.366-2.5280.1751010.1232106X-RAY DIFFRACTION100
2.528-2.7280.23850.1331954X-RAY DIFFRACTION100
2.728-2.9850.183830.1351815X-RAY DIFFRACTION100
2.985-3.3320.215850.1591641X-RAY DIFFRACTION100
3.332-3.8370.155600.1321456X-RAY DIFFRACTION100
3.837-4.6740.148490.121259X-RAY DIFFRACTION99.9236
4.674-6.5050.185540.144970X-RAY DIFFRACTION99.7079
6.505-100.153510.139564X-RAY DIFFRACTION99.0338

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