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- PDB-9j5d: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido... -

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Basic information

Entry
Database: PDB / ID: 9j5d
TitleESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with dimethyl phthalate on surface
ComponentsAlpha/beta hydrolase fold-3 domain-containing protein
KeywordsHYDROLASE / ESTS1 / phthalate ester degrading esterase / dimethyl 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
ACETYL GROUP / 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)34,8299
Polymers34,1771
Non-polymers6538
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.038, 108.038, 44.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 198 molecules

#2: Chemical ChemComp-TIK / dimethyl benzene-1,2-dicarboxylate / Dimethyl phthalate


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 45.43 %
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: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→27.7 Å / Num. obs: 58638 / % possible obs: 100 % / Redundancy: 3.02 % / Rrim(I) all: 0.158 / Net I/σ(I): 8.6
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 58638 / Rrim(I) all: 1 / % 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: 1.5→25.562 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.726 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2002 2351 4.931 %
Rwork0.1512 45327 -
all0.154 --
obs-47678 99.878 %
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: 18.264 Å2
Baniso -1Baniso -2Baniso -3
1-0.702 Å20.351 Å2-0 Å2
2--0.702 Å2-0 Å2
3----2.276 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 44 190 2537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122439
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162226
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6573325
X-RAY DIFFRACTIONr_angle_other_deg0.491.5575185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.7415.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43610364
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.94510108
X-RAY DIFFRACTIONr_chiral_restr0.0750.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
X-RAY DIFFRACTIONr_nbd_refined0.2250.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22022
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21197
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.213
X-RAY DIFFRACTIONr_nbd_other0.2330.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.214
X-RAY DIFFRACTIONr_mcbond_it1.4480.8551204
X-RAY DIFFRACTIONr_mcbond_other1.4480.8561205
X-RAY DIFFRACTIONr_mcangle_it1.761.2821504
X-RAY DIFFRACTIONr_mcangle_other1.7631.2841505
X-RAY DIFFRACTIONr_scbond_it2.2811.1261235
X-RAY DIFFRACTIONr_scbond_other2.281.1271236
X-RAY DIFFRACTIONr_scangle_it2.5951.5881817
X-RAY DIFFRACTIONr_scangle_other2.5941.5891818
X-RAY DIFFRACTIONr_lrange_it2.66414.8962702
X-RAY DIFFRACTIONr_lrange_other2.65114.1692664
X-RAY DIFFRACTIONr_rigid_bond_restr3.4134665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2891800.24133310.24435110.940.9551000.245
1.539-1.5810.281640.21732050.2233690.9450.9641000.218
1.581-1.6270.241640.19331580.19533220.9610.9721000.19
1.627-1.6760.2111660.17430290.17631950.9710.9791000.169
1.676-1.7310.231500.15330070.15631570.9630.9841000.146
1.731-1.7920.2191770.14928370.15330140.9720.9851000.14
1.792-1.8590.241500.14927780.15429280.960.9861000.138
1.859-1.9340.181380.1426810.14228190.980.9881000.128
1.934-2.020.211480.13325450.13726930.9680.9891000.122
2.02-2.1180.1881360.12924680.13226050.9790.99199.96160.12
2.118-2.2310.2031150.13423300.13824470.9780.98999.91830.124
2.231-2.3660.181010.12922160.13123200.9790.9999.87070.122
2.366-2.5270.1971010.14521050.14722080.9790.98899.90940.139
2.527-2.7280.229840.15419530.15720430.9690.98699.70630.154
2.728-2.9850.199810.15418040.15618920.9750.98699.630.157
2.985-3.3310.191820.15516370.15717260.9790.98599.59440.162
3.331-3.8360.167610.14514510.14615140.9810.98899.86790.157
3.836-4.6720.167490.13412570.13513130.9860.99199.46690.152
4.672-6.4990.168530.1539700.15410270.9860.98999.61050.179
6.499-25.5620.186510.1575640.1596190.9840.98599.35380.176
Refinement TLS params.Method: refined / Origin x: -12.5212 Å / Origin y: -37.6821 Å / Origin z: 0.2225 Å
111213212223313233
T0.013 Å2-0.0042 Å20.0019 Å2-0.0357 Å20.0049 Å2--0.0574 Å2
L1.3648 °2-0.0819 °2-0.1728 °2-0.7969 °2-0.0996 °2--1.8446 °2
S-0.0265 Å °-0.0406 Å °0.0055 Å °0.0202 Å °0.0032 Å °-0.0278 Å °-0.1394 Å °0.0049 Å °0.0232 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 304
2X-RAY DIFFRACTION1A401 - 408

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