PDB-9hyd: PETaseSM14 from marine-sponge Streptomyces sp.

ID or keywords:

Entry

Database: PDB / ID: 9hyd

Title

PETaseSM14 from marine-sponge Streptomyces sp.

Components

cutinase

Keywords

HYDROLASE / PETase / Polyethylene Terephthalate / salt tolerance

Function / homology

Cutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Alpha/beta hydrolase

Function and homology information

Biological species

Streptomyces sp. SM14 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.425 Å

Authors

Bhattacharya, S. / Castagna, R. / Parisini, E.

Funding support

1items

Citation

Journal: Acs Sustain Chem Eng / Year: 2025
Title: Functional and Structural Characterization of PETase SM14 from Marine-Sponge Streptomyces sp. Active on Polyethylene Terephthalate.
Authors: Carletti, A. / Bhattacharya, S. / Pedroni, S. / Berto, M. / Bonettini, R. / Castagna, R. / Parisini, E. / Di Rocco, G.

History

Deposition	Jan 9, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hyd.cif.gz	284.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9hyd.ent.gz	176.8 KB	Display	PDB format
PDBx/mmJSON format	9hyd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hyd_validation.pdf.gz	422.2 KB	Display	wwPDB validaton report
Full document	9hyd_full_validation.pdf.gz	423.6 KB	Display
Data in XML	9hyd_validation.xml.gz	16.9 KB	Display
Data in CIF	9hyd_validation.cif.gz	24.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/9hyd ftp://data.pdbj.org/pub/pdb/validation_reports/hy/9hyd	HTTPS FTP

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Related structure data

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: cutinase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	96.983, 96.983, 44.815
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	cutinase Mass: 28869.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SM14 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A679PDB4, cutinase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.11 Å³/Da / Density % sol: 41.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7133 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 30, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.7133 Å / Relative weight: 1
Reflection	Resolution: 1.425→83.99 Å / Num. obs: 45062 / % possible obs: 100 % / Redundancy: 21.3 % / CC_1/2: 0.999 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.425→1.45 Å / Num. unique obs: 2230 / CC_1/2: 0.305

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
autoPROC		data reduction
autoPROC		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.425→83.99 Å / Cor.coef. F_o:F_c: 0.986 / Cor.coef. F_o:F_c free: 0.968 / SU B: 4.998 / SU ML: 0.076 / Cross valid method: NONE / ESU R: 0.065 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2018	2279	5.058 %
R_work	0.1363	42782	-
all	0.14	-	-
obs	-	45061	99.971 %

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: 22.788 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.167 Å²	0.084 Å²	0 Å²
2-	-	0.167 Å²	-0 Å²
3-	-	-	-0.543 Å²

Refinement step

Cycle: LAST / Resolution: 1.425→83.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1994	0	30	296	2320

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2097
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.016	1832
X-RAY DIFFRACTION	r_angle_refined_deg	1.623	1.652	2851
X-RAY DIFFRACTION	r_angle_other_deg	0.575	1.559	4275
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.789	5	268
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.196	5	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.218	10	313
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.515	10	98
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	307
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2493
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	439
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	400
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	1850
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1031
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1090
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.211	0.2	239
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.275	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	36
X-RAY DIFFRACTION	r_mcbond_it	3.051	2.341	1054
X-RAY DIFFRACTION	r_mcbond_other	3.043	2.34	1053
X-RAY DIFFRACTION	r_mcangle_it	3.296	3.515	1322
X-RAY DIFFRACTION	r_mcangle_other	3.295	3.516	1323
X-RAY DIFFRACTION	r_scbond_it	5.697	2.652	1043
X-RAY DIFFRACTION	r_scbond_other	5.695	2.653	1044
X-RAY DIFFRACTION	r_scangle_it	5.827	3.862	1527
X-RAY DIFFRACTION	r_scangle_other	5.825	3.863	1528
X-RAY DIFFRACTION	r_lrange_it	6.108	45.588	2500
X-RAY DIFFRACTION	r_lrange_other	5.264	39.539	2392
X-RAY DIFFRACTION	r_rigid_bond_restr	5.932	3	3929

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
1.425-1.462	0.356	160	0.355	3152	0.355	3312	0.702	0.701	100	0.359
1.462-1.502	0.352	179	0.307	3028	0.309	3207	0.9	0.922	100	0.311
1.502-1.546	0.286	187	0.273	2968	0.273	3155	0.938	0.942	100	0.275
1.546-1.593	0.306	172	0.25	2893	0.254	3065	0.934	0.952	100	0.249
1.593-1.645	0.233	139	0.195	2814	0.196	2953	0.957	0.972	100	0.19
1.645-1.703	0.249	144	0.177	2730	0.181	2874	0.958	0.977	100	0.166
1.703-1.767	0.261	124	0.173	2603	0.177	2727	0.954	0.979	100	0.16
1.767-1.84	0.236	128	0.141	2542	0.145	2670	0.965	0.987	100	0.125
1.84-1.921	0.29	109	0.143	2450	0.149	2559	0.955	0.987	100	0.126
1.921-2.015	0.192	116	0.115	2347	0.118	2463	0.977	0.992	100	0.101
2.015-2.124	0.196	126	0.116	2203	0.12	2329	0.976	0.991	100	0.104
2.124-2.253	0.22	87	0.113	2098	0.117	2185	0.97	0.992	100	0.103
2.253-2.408	0.212	111	0.098	1967	0.104	2078	0.972	0.994	100	0.092
2.408-2.601	0.172	107	0.104	1831	0.108	1938	0.982	0.993	100	0.099
2.601-2.849	0.173	104	0.106	1671	0.11	1787	0.982	0.993	99.3285	0.104
2.849-3.185	0.183	84	0.111	1527	0.115	1611	0.98	0.993	100	0.114
3.185-3.676	0.161	68	0.117	1380	0.119	1448	0.984	0.993	100	0.124
3.676-4.501	0.138	53	0.101	1155	0.103	1208	0.988	0.994	100	0.117
4.501-6.356	0.176	57	0.13	904	0.132	961	0.987	0.993	100	0.156
6.356-83.99	0.221	24	0.167	521	0.169	546	0.981	0.986	99.8168	0.208

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