PDB-8ve9: IsPETase - ACCCETN mutant - CombiPETase

ID or keywords:

Entry

Database: PDB / ID: 8ve9

Title

IsPETase - ACCCETN mutant - CombiPETase

Components

Poly(ethylene terephthalate) hydrolase

Keywords

HYDROLASE / PETase / protein engineering

Function / homology

Function and homology information

acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function

Biological species

Piscinibacter sakaiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Joho, Y. / Royan, S. / Newton, S. / Caputo, A.T. / Ardevol Grau, A. / Jackson, C.

Funding support

Australia, 1items

Citation

Journal: Chembiochem / Year: 2024
Title: Enhancing PET Degrading Enzymes: A Combinatory Approach.
Authors: Joho, Y. / Royan, S. / Caputo, A.T. / Newton, S. / Peat, T.S. / Newman, J. / Jackson, C. / Ardevol, A.

History

Deposition	Dec 18, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release
Revision 1.1	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	8ve9.cif.gz	115.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ve9.ent.gz	85.1 KB	Display	PDB format
PDBx/mmJSON format	8ve9.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/ve/8ve9 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/8ve9	HTTPS FTP

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Related structure data

Related structure data	8vekC 8velC 8vemC 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
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Poly(ethylene terephthalate) hydrolase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.475, 68.259, 78.592
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme Mass: 28647.842 Da / Num. of mol.: 1 / Mutation: K95N, S136E, A179C, D186A, S214T, N233C, S282C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Piscinibacter sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.36 Å³/Da / Density % sol: 47.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.71 Details: 22.4% (w/v) PEG 3350, 0.23 M TMAO, 0.1 M trisodium citrate-citric acid pH 3.71

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95373 Å / Relative weight: 1
Reflection	Resolution: 1.6→51.588 Å / Num. obs: 36462 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC_1/2: 0.999 / Net I/σ(I): 14.7
Reflection shell	Resolution: 1.6→1.6 Å / Num. unique obs: 1794 / CC_1/2: 0.972

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
autoPROC	1.0.5	data reduction
autoPROC	1.0.5	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→51.588 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.968 / WR_factor R_free: 0.161 / WR_factor R_work: 0.139 / SU B: 1.507 / SU ML: 0.05 / Average fsc free: 0.975 / Average fsc work: 0.9814 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1717	1823	5 %
R_work	0.145	34639	-
all	0.146	-	-
obs	-	36462	99.765 %

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: 21.262 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.071 Å²	-0 Å²	-0 Å²
2-	-	0.11 Å²	-0 Å²
3-	-	-	0.962 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→51.588 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1928	0	13	197	2138

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2030
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1853
X-RAY DIFFRACTION	r_angle_refined_deg	1.846	1.769	2779
X-RAY DIFFRACTION	r_angle_other_deg	0.648	1.715	4283
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.576	5	282
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.624	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.285	10	300
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.025	10	76
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	313
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2486
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	480
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	421
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	1721
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1034
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1064
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.25	0.2	123
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	1.849	2.176	1071
X-RAY DIFFRACTION	r_mcbond_other	1.853	2.177	1071
X-RAY DIFFRACTION	r_mcangle_it	2.419	3.898	1342
X-RAY DIFFRACTION	r_mcangle_other	2.418	3.901	1343
X-RAY DIFFRACTION	r_scbond_it	2.751	2.399	959
X-RAY DIFFRACTION	r_scbond_other	2.749	2.402	960
X-RAY DIFFRACTION	r_scangle_it	3.999	4.299	1427
X-RAY DIFFRACTION	r_scangle_other	3.998	4.3	1428
X-RAY DIFFRACTION	r_lrange_it	5	23.175	2327
X-RAY DIFFRACTION	r_lrange_other	4.826	21.816	2299

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
1.6-1.642	0.294	142	0.243	2510	0.245	2675	0.926	0.953	99.1402	0.227
1.642-1.686	0.22	142	0.231	2423	0.231	2584	0.965	0.96	99.2647	0.211
1.686-1.735	0.245	113	0.198	2406	0.201	2522	0.96	0.971	99.8811	0.175
1.735-1.789	0.197	114	0.183	2330	0.184	2454	0.974	0.977	99.5925	0.159
1.789-1.847	0.194	120	0.174	2237	0.176	2366	0.976	0.979	99.6196	0.149
1.847-1.912	0.185	114	0.158	2179	0.159	2300	0.976	0.983	99.6957	0.134
1.912-1.984	0.177	114	0.143	2113	0.145	2232	0.98	0.987	99.776	0.123
1.984-2.065	0.155	109	0.137	2066	0.138	2177	0.985	0.988	99.9081	0.118
2.065-2.157	0.163	104	0.128	1933	0.13	2039	0.985	0.99	99.9019	0.113
2.157-2.262	0.144	101	0.122	1881	0.123	1983	0.985	0.991	99.9496	0.108
2.262-2.384	0.167	99	0.119	1784	0.122	1884	0.983	0.991	99.9469	0.107
2.384-2.528	0.146	90	0.124	1707	0.125	1797	0.987	0.991	100	0.114
2.528-2.702	0.161	79	0.122	1595	0.124	1674	0.983	0.991	100	0.114
2.702-2.918	0.146	73	0.131	1516	0.131	1591	0.989	0.989	99.8743	0.122
2.918-3.195	0.147	80	0.132	1360	0.133	1440	0.988	0.989	100	0.129
3.195-3.571	0.16	66	0.138	1276	0.139	1342	0.985	0.989	100	0.138
3.571-4.12	0.158	51	0.14	1120	0.141	1171	0.987	0.989	100	0.149
4.12-5.038	0.171	50	0.141	976	0.142	1026	0.982	0.989	100	0.156
5.038-7.091	0.198	38	0.182	766	0.183	805	0.983	0.986	99.8758	0.198
7.091-51.588	0.245	24	0.159	461	0.163	486	0.968	0.983	99.7942	0.193

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