PDB-8qrj: LCC-ICCG PETase mutant H218Y

ID or keywords:

Entry

Database: PDB / ID: 8qrj

Title

LCC-ICCG PETase mutant H218Y

Components

Leaf-branch compost cutinase

Keywords

HYDROLASE / LCC / PETase / direct enzyme evolution

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: 1.42 Å

Authors

Orr, G. / Niv, Y. / Barakat, M. / Boginya, A. / Dessau, M. / Afriat-Jurnou, L.

Funding support

Israel, 1items

Citation

Journal: Biotechnol J / Year: 2024
Title: Streamlined screening of extracellularly expressed PETase libraries for improved polyethylene terephthalate degradation.
Authors: Orr, G. / Niv, Y. / Barakat, M. / Boginya, A. / Dessau, M. / Afriat-Jurnou, L.

History

Deposition	Oct 9, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 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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PDBx/mmCIF format	8qrj.cif.gz	123.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8qrj.ent.gz	92.6 KB	Display	PDB format
PDBx/mmJSON format	8qrj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8qrj_validation.pdf.gz	657.8 KB	Display	wwPDB validaton report
Full document	8qrj_full_validation.pdf.gz	659.6 KB	Display
Data in XML	8qrj_validation.xml.gz	18.8 KB	Display
Data in CIF	8qrj_validation.cif.gz	28 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/8qrj ftp://data.pdbj.org/pub/pdb/validation_reports/qr/8qrj	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)

Deposited unit

A: Leaf-branch compost cutinase

hetero molecules

31.8 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)	81.900, 94.510, 80.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-682- HOH

#1: Protein	Leaf-branch compost cutinase Mass: 31412.410 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
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₃₀O₈ / Comment: precipitant*YM
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.49 Å³/Da / Density % sol: 50.67 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 7.3 / Details: 20% PEG 3350, 0.2 M Na-formate pH=7.3

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID30B / Wavelength: 0.8731 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.8731 Å / Relative weight: 1

Reflection

Resolution: 1.42→50 Å / Num. obs: 93953 / % possible obs: 82 % / Redundancy: 1.77 % / CC_1/2: 0.994 / R_merge(I) obs: 0.099 / R_rim(I) all: 0.13 / Net I/σ(I): 4.65

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.42-1.46	0.894	6863	0.314	1.175	1
1.46-1.5	0.766	6526	0.409	1.009	1
1.5-1.54	0.587	6221	0.563	0.772	1
1.54-1.59	0.516	6405	0.615	0.676	1
1.59-1.64	0.464	6213	0.674	0.612	1
1.64-1.7	0.363	5973	0.744	0.48	1
1.7-1.76	0.313	5937	0.802	0.41	1
1.76-1.83	0.257	5753	0.863	0.336	1
1.83-1.91	0.202	5406	0.905	0.264	1
1.91-2.01	0.168	5262	0.931	0.22	1
2.01-2.12	0.13	4969	0.958	0.171	1
2.12-2.25	0.111	4750	0.971	0.146	1
2.25-2.4	0.1	4332	0.975	0.132	1
2.4-2.59	0.084	3911	0.98	0.112	1
2.59-2.84	0.077	3650	0.984	0.101	1
2.84-3.18	0.062	3283	0.989	0.081	1
3.18-3.67	0.045	2907	0.993	0.059	1
3.67-4.49	0.038	2550	0.996	0.049	1
4.49-6.35	0.039	2001	0.996	0.051	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.42→49.17 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1822	2868	5.07 %
R_work	0.1669	-	-
obs	0.1676	56565	95.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.42→49.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1941	0	27	442	2410

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2046
X-RAY DIFFRACTION	f_angle_d	0.826	2799
X-RAY DIFFRACTION	f_dihedral_angle_d	11.49	738
X-RAY DIFFRACTION	f_chiral_restr	0.078	315
X-RAY DIFFRACTION	f_plane_restr	0.01	365

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.42-1.44	0.3559	134	0.3076	2631	X-RAY DIFFRACTION	95
1.47-1.5	0.3125	153	0.2696	2599	X-RAY DIFFRACTION	93
1.5-1.53	0.2631	137	0.2588	2601	X-RAY DIFFRACTION	93
1.53-1.56	0.2592	144	0.248	2628	X-RAY DIFFRACTION	94
1.56-1.6	0.2669	143	0.2447	2693	X-RAY DIFFRACTION	96
1.6-1.64	0.2693	140	0.2352	2653	X-RAY DIFFRACTION	95
1.64-1.68	0.2567	150	0.2174	2625	X-RAY DIFFRACTION	94
1.68-1.73	0.2056	149	0.1977	2704	X-RAY DIFFRACTION	97
1.73-1.79	0.2217	142	0.1814	2729	X-RAY DIFFRACTION	97
1.79-1.85	0.1797	132	0.1718	2698	X-RAY DIFFRACTION	96
1.85-1.93	0.2018	144	0.1713	2724	X-RAY DIFFRACTION	97
1.93-2.01	0.185	148	0.1615	2701	X-RAY DIFFRACTION	96
2.02-2.12	0.1744	146	0.1459	2714	X-RAY DIFFRACTION	96
2.12-2.25	0.1564	136	0.1373	2724	X-RAY DIFFRACTION	96
2.25-2.43	0.1456	153	0.1442	2710	X-RAY DIFFRACTION	96
2.43-2.67	0.1732	162	0.1498	2658	X-RAY DIFFRACTION	94
2.67-3.06	0.1793	154	0.1506	2701	X-RAY DIFFRACTION	95
3.06-3.85	0.1426	125	0.1398	2716	X-RAY DIFFRACTION	93
3.85-49.17	0.1273	146	0.1377	2851	X-RAY DIFFRACTION	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.1431	-0.1389	-0.0013	1.7911	0.3859	1.4497	0.0079	0.0169	0.095	-0.0649	-0.0028	0.0721	-0.0448	-0.0395	-0.006	0.0916	0.0099	0.0005	0.1026	0.0171	0.0922	25.4305	25.6475	23.3517
2	0.7378	-0.3049	0.2825	2.7892	-0.9622	0.8028	0.017	0.0114	-0.0037	0.0319	0.0609	0.167	0.0269	-0.1076	-0.0797	0.112	0.002	0.0006	0.1214	0.0027	0.1059	21.8365	16.4551	29.2542
3	0.2354	-0.113	0.2802	7.8782	-2.008	1.3097	0.0377	-0.0196	-0.0468	-0.1029	0.0308	0.2383	0.1546	-0.0633	-0.0794	0.1143	0.0002	0.0013	0.11	0.0052	0.1129	26.3844	10.0078	26.5078
4	0.2709	0.3191	-0.383	1.2247	-0.3555	0.5514	0.0281	0.0165	-0.015	-0.0723	-0.0359	-0.0251	0.0208	0.0186	0.0257	0.1066	0.006	-0.0038	0.1292	0.0042	0.1137	34.4081	16.6967	21.7311
5	0.9619	0.0529	-0.5955	0.8518	-0.0637	1.5944	-0.0034	-0.0673	-0.0189	0.0612	-0.0036	-0.0332	0.0685	0.0955	0.0139	0.0958	0.0044	-0.0046	0.0993	0.0028	0.1077	32.2367	14.4275	42.021
6	0.7408	0.3195	0.3545	1.8108	-0.0077	2.6709	0.05	-0.0575	0.1307	-0.0309	-0.0217	0.1116	0.0836	-0.221	-0.0054	0.0732	-0.0113	0.0107	0.1128	-0.0072	0.132	16.0059	15.9893	40.8143
7	0.6051	0.2911	-0.7132	0.8719	-0.6465	2.2565	0.0861	-0.0962	0.1067	0.092	-0.0367	-0.019	-0.2223	0.1221	-0.0578	0.1162	-0.0062	0.012	0.1074	-0.019	0.1169	28.5148	29.2065	41.9501

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 36 through 87 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 113 through 127 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 158 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 159 through 237 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 238 through 249 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 250 through 292 )

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