PDB-9j1v: ESTS1 phthalate ester degrading esterase from Sulfobacillus acido...

ID or keywords:

Entry

Database: PDB / ID: 9j1v

Title

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Monomethyl phthalate

Components

Alpha/beta hydrolase fold-3 domain-containing protein

Keywords

HYDROLASE / ESTS1 / phthalate ester degrading esterase / Sulfobacillus acidophilus / Monomethyl phthalate

Function / homology

Function and homology information

triacylglycerol lipase / hydrolase activity
Similarity search - Function

Biological species

Sulfobacillus acidophilus DSM 10332 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Verma, S. / Kumar, P.

Funding support

India, 1items

Citation

Journal: 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

Deposition	Aug 5, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 19, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9j1v.cif.gz	313.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9j1v.ent.gz	195.4 KB	Display	PDB format
PDBx/mmJSON format	9j1v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j1/9j1v ftp://data.pdbj.org/pub/pdb/validation_reports/j1/9j1v	HTTPS FTP

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Related structure data

Related structure data	8w98C 8ze9C 9j1eC 9j1gC 9j57C 9j58C 9j59C 9j5aC 9j5bC 9j5cC 9j5dC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha/beta hydrolase fold-3 domain-containing protein

hetero molecules

35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	107.984, 107.984, 44.782
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

#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-R3O / 2-methoxycarbonylbenzoic acid / monomethyl phthalate Mass: 180.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₈O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.66 % / Description: Rod Shape
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion Details: Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 18, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2→27.74 Å / Num. obs: 20399 / % possible obs: 100 % / Redundancy: 2.8 % / R_merge(I) obs: 0.143 / Net I/σ(I): 18.8
Reflection shell	Resolution: 2→2.05 Å / R_merge(I) obs: 0.517 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 20399

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
CrysalisPro		data reduction
CrysalisPro		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→25.95 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.928 / SU B: 7.609 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.201	963	4.725 %
R_work	0.1082	19419	-
all	0.113	-	-
obs	-	20382	99.892 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 19.039 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.589 Å²	0.295 Å²	0 Å²
2-	-	0.589 Å²	-0 Å²
3-	-	-	-1.912 Å²

Refinement step

Cycle: LAST / Resolution: 2→25.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2279	0	67	115	2461

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	2408
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.016	2185
X-RAY DIFFRACTION	r_angle_refined_deg	1.672	1.658	3274
X-RAY DIFFRACTION	r_angle_other_deg	0.576	1.556	5078
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.516	5	295
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.774	5.714	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.125	10	349
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.137	10	106
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	353
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2763
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	477
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	509
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	2151
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1175
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1221
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	115
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.184	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	54
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.118	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.99	1.637	1180
X-RAY DIFFRACTION	r_mcbond_other	3.969	1.636	1180
X-RAY DIFFRACTION	r_mcangle_it	4.774	2.456	1472
X-RAY DIFFRACTION	r_mcangle_other	4.773	2.459	1473
X-RAY DIFFRACTION	r_scbond_it	6.822	2.276	1228
X-RAY DIFFRACTION	r_scbond_other	6.811	2.271	1226
X-RAY DIFFRACTION	r_scangle_it	7.835	3.175	1801
X-RAY DIFFRACTION	r_scangle_other	7.834	3.177	1802
X-RAY DIFFRACTION	r_lrange_it	7.083	24.521	2669
X-RAY DIFFRACTION	r_lrange_other	7.061	24.291	2658
X-RAY DIFFRACTION	r_rigid_bond_restr	9.008	3	4593

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2-2.052	0.248	74	0.101	1423	0.108	1497	0.96	0.993	100	0.086
2.052-2.108	0.235	53	0.084	1387	0.09	1440	0.969	0.995	100	0.071
2.108-2.168	0.173	54	0.081	1355	0.085	1409	0.979	0.996	100	0.069
2.168-2.234	0.225	46	0.085	1326	0.089	1373	0.972	0.995	99.9272	0.073
2.234-2.307	0.227	93	0.097	1222	0.106	1315	0.968	0.994	100	0.084
2.307-2.387	0.254	64	0.097	1235	0.105	1299	0.965	0.994	100	0.085
2.387-2.477	0.259	63	0.104	1175	0.112	1238	0.96	0.993	100	0.092
2.477-2.577	0.194	39	0.099	1161	0.102	1200	0.978	0.994	100	0.089
2.577-2.69	0.198	58	0.108	1087	0.113	1145	0.979	0.993	100	0.096
2.69-2.82	0.216	71	0.107	1033	0.114	1104	0.974	0.993	100	0.097
2.82-2.971	0.207	59	0.109	991	0.114	1050	0.975	0.993	100	0.1
2.971-3.148	0.197	43	0.112	964	0.115	1007	0.971	0.992	100	0.105
3.148-3.362	0.229	41	0.124	890	0.128	931	0.964	0.991	100	0.119
3.362-3.627	0.173	61	0.115	820	0.119	882	0.981	0.993	99.8866	0.114
3.627-3.965	0.131	39	0.118	763	0.119	802	0.99	0.992	100	0.119
3.965-4.42	0.179	24	0.103	721	0.105	747	0.98	0.994	99.7323	0.106
4.42-5.079	0.161	32	0.112	624	0.115	658	0.989	0.994	99.696	0.117
5.079-6.162	0.235	27	0.134	531	0.138	558	0.974	0.992	100	0.137
6.162-8.479	0.117	17	0.136	431	0.135	449	0.992	0.989	99.7773	0.142
8.479-25.95	0.2	5	0.167	279	0.167	286	0.98	0.979	99.3007	0.19

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