PDB-8cmv: Engineered PETase enzyme from LCC - C09 mutant

ID or keywords:

Entry

Database: PDB / ID: 8cmv

Title

Engineered PETase enzyme from LCC - C09 mutant

Components

Leaf-branch compost cutinase

Keywords

HYDROLASE / Plastic degradation / Thermal stablization / MHET / BHET / TPA

Function / homology

Function and homology information

acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function

Biological species

unidentified prokaryotic organism (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.28 Å

Authors

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

Funding support

Latvia, 1items

Citation

Journal: Biorxiv / Year: 2024
Title: Development of a highly active engineered PETase enzyme for polyester degradation
Authors: Bhattacharya, S. / Castagna, R. / Estiri, H. / Upmanis, T. / Ricci, A. / Gautieri, A. / Parisini, E.

History

Deposition	Feb 21, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 25, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cmv.cif.gz	119.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8cmv.ent.gz	89.2 KB	Display	PDB format
PDBx/mmJSON format	8cmv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cmv_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8cmv_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8cmv_validation.xml.gz	14.5 KB	Display
Data in CIF	8cmv_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cm/8cmv ftp://data.pdbj.org/pub/pdb/validation_reports/cm/8cmv	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
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (3) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Leaf-branch compost cutinase

hetero molecules

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

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	108.876, 108.876, 35.402
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Leaf-branch compost cutinase / LC-cutinase / LCC / PET-digesting enzyme / Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase Mass: 32759.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified prokaryotic organism (environmental samples) Production host: Escherichia coli (E. coli) References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.85 Å³/Da / Density % sol: 33.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Sodium citrate tribasic dihydrate 1M Isopropanol 20% PEG 4K 20%

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7338 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.7338 Å / Relative weight: 1
Reflection	Resolution: 1.28→54.497 Å / Num. obs: 62178 / % possible obs: 100 % / Redundancy: 20.8 % / CC_1/2: 0.998 / Net I/σ(I): 6.5
Reflection shell	Resolution: 1.28→1.302 Å / Num. unique obs: 3088 / CC_1/2: 0.346

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
Aimless		data scaling
MLPHARE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.28→54.497 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.973 / WR_factor R_free: 0.181 / WR_factor R_work: 0.158 / SU B: 1.004 / SU ML: 0.04 / Average fsc free: 0.9649 / Average fsc work: 0.9697 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1871	3158	5.079 %
R_work	0.1634	59019	-
all	0.165	-	-
obs	-	62177	99.998 %

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: 13.685 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.113 Å²	0.056 Å²	0 Å²
2-	-	0.113 Å²	-0 Å²
3-	-	-	-0.366 Å²

Refinement step

Cycle: LAST / Resolution: 1.28→54.497 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1970	0	28	248	2246

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.011	2093
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1954
X-RAY DIFFRACTION	r_angle_refined_deg	1.711	1.652	2867
X-RAY DIFFRACTION	r_angle_other_deg	0.612	1.569	4493
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.591	5	277
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.464	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.824	10	310
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.89	10	89
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	326
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2529
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	511
X-RAY DIFFRACTION	r_nbd_refined	0.237	0.2	413
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	1870
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1050
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1110
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.218	0.2	176
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.242	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.153	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	1.397	1.269	1051
X-RAY DIFFRACTION	r_mcbond_other	1.388	1.268	1051
X-RAY DIFFRACTION	r_mcangle_it	2.152	2.271	1317
X-RAY DIFFRACTION	r_mcangle_other	2.162	2.276	1318
X-RAY DIFFRACTION	r_scbond_it	2.362	1.57	1042
X-RAY DIFFRACTION	r_scbond_other	2.361	1.573	1043
X-RAY DIFFRACTION	r_scangle_it	3.465	2.737	1540
X-RAY DIFFRACTION	r_scangle_other	3.463	2.739	1541
X-RAY DIFFRACTION	r_lrange_it	5.372	17.533	2440
X-RAY DIFFRACTION	r_lrange_other	5.371	17.541	2441

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

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	WR_factor R_work
1.28-1.313	0.309	238	0.329	4360	0.328	4598	0.939	0.929	0.334
1.313-1.349	0.32	241	0.302	4166	0.303	4407	0.926	0.933	0.307
1.349-1.388	0.302	224	0.293	4100	0.294	4324	0.936	0.936	0.297
1.388-1.431	0.286	203	0.257	4005	0.258	4208	0.941	0.95	0.261
1.431-1.478	0.24	221	0.228	3875	0.229	4096	0.957	0.962	0.23
1.478-1.529	0.226	202	0.206	3744	0.207	3946	0.967	0.972	0.205
1.529-1.587	0.209	191	0.187	3603	0.188	3794	0.972	0.977	0.182
1.587-1.652	0.23	164	0.182	3505	0.184	3669	0.968	0.979	0.174
1.652-1.725	0.207	201	0.17	3311	0.172	3512	0.975	0.983	0.159
1.725-1.809	0.184	177	0.158	3210	0.159	3387	0.978	0.986	0.145
1.809-1.907	0.156	166	0.146	3049	0.146	3215	0.987	0.988	0.133
1.907-2.023	0.178	151	0.137	2872	0.139	3023	0.981	0.988	0.126
2.023-2.162	0.185	140	0.13	2728	0.133	2868	0.979	0.99	0.123
2.162-2.335	0.168	124	0.131	2550	0.133	2674	0.983	0.99	0.127
2.335-2.557	0.153	120	0.132	2339	0.133	2459	0.987	0.989	0.131
2.557-2.859	0.173	116	0.132	2114	0.134	2230	0.983	0.989	0.136
2.859-3.299	0.179	77	0.129	1910	0.131	1987	0.983	0.99	0.135
3.299-4.037	0.125	107	0.128	1577	0.128	1684	0.992	0.991	0.143
4.037-5.694	0.143	59	0.13	1270	0.131	1329	0.989	0.991	0.158
5.694-54.497	0.168	36	0.169	731	0.169	767	0.994	0.984	0.207

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