PDB-9qys: Crystal structure of leaf branch compost cutinase variant ICCG L5...

ID or keywords:

Entry

Database: PDB / ID: 9qys

Title

Crystal structure of leaf branch compost cutinase variant ICCG L50Y Q238K

Components

Leaf-branch compost cutinase

Keywords

HYDROLASE / cutinase / PET depolymerase

Function / homology

Function and homology information

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

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Bischoff, D. / Walla, B. / Janowski, R. / Niessing, D. / Weuster-Botz, D.

Funding support

Germany, 1items

Citation

Journal: Bioengineering (Basel) / Year: 2025
Title: Application of a Rational Crystal Contact Engineering Strategy on a Poly(ethylene terephthalate)-Degrading Cutinase.
Authors: Walla, B. / Dietrich, A.M. / Brames, E. / Bischoff, D. / Fritzsche, S. / Castiglione, K. / Janowski, R. / Niessing, D. / Weuster-Botz, D.

History

Deposition	Apr 20, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jul 9, 2025	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qys.cif.gz	71.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9qys.ent.gz	49 KB	Display	PDB format
PDBx/mmJSON format	9qys.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/qy/9qys ftp://data.pdbj.org/pub/pdb/validation_reports/qy/9qys	HTTPS FTP

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Related structure data

Related structure data	9qypC 9qyqC 9qyrC 9qytC 9qyuC 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 (3)

Deposited unit

A: Leaf-branch compost cutinase

hetero molecules

29 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, monomer

Unit cell

Length a, b, c (Å)	97.32, 97.32, 72.48
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-61- TYR

#1: Protein	Leaf-branch compost cutinase / LC-cutinase / LCC / PET-digesting enzyme / Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase Mass: 28917.379 Da / Num. of mol.: 1 / Mutation: L50Y Q238K Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.97 Å³/Da / Density % sol: 58.55 %
Crystal grow	Temperature: 293 K / Method: microbatch Details: 10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→48.66 Å / Num. obs: 870560 / % possible obs: 100 % / Redundancy: 26.49 % / CC_1/2: 1 / Net I/σ(I): 27.92
Reflection shell	Resolution: 1.8→1.91 Å / Num. unique obs: 5189 / CC_1/2: 0.767

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
XDS	Jun 30, 2024	data reduction
XDS	Jun 30, 2024	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→48.66 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.96 / SU B: 2.984 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.103 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2129	1637	5.002 %
R_work	0.1749	31087	-
all	0.177	-	-
obs	-	32724	99.701 %

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: 37.265 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.433 Å²	0 Å²	0 Å²
2-	-	-1.433 Å²	0 Å²
3-	-	-	2.867 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→48.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1943	0	4	206	2153

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2027
X-RAY DIFFRACTION	r_angle_refined_deg	1.927	1.783	2778
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.964	5	262
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.986	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.542	10	290
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.879	10	85
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	311
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1591
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	1005
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	1404
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.202	0.2	195
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.214	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.201	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	3.341	3.516	1042
X-RAY DIFFRACTION	r_mcangle_it	4.08	6.286	1306
X-RAY DIFFRACTION	r_scbond_it	4.477	3.697	985
X-RAY DIFFRACTION	r_scangle_it	5.64	6.687	1472
X-RAY DIFFRACTION	r_lrange_it	10.889	39.483	3275

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
1.8-1.847	0.439	117	0.377	2208	0.38	2369	0.89	0.913	98.1427	0.361
1.847-1.897	0.369	116	0.311	2208	0.313	2333	0.873	0.92	99.6142	0.282
1.897-1.952	0.28	112	0.27	2131	0.271	2244	0.928	0.935	99.9554	0.238
1.952-2.012	0.271	110	0.228	2090	0.23	2201	0.945	0.958	99.9546	0.19
2.012-2.078	0.278	107	0.217	2036	0.22	2143	0.941	0.963	100	0.179
2.078-2.151	0.269	103	0.209	1950	0.212	2056	0.954	0.97	99.8541	0.176
2.151-2.232	0.212	99	0.188	1891	0.189	1990	0.971	0.976	100	0.156
2.232-2.323	0.246	97	0.174	1839	0.177	1937	0.956	0.98	99.9484	0.145
2.323-2.426	0.231	93	0.171	1770	0.173	1863	0.959	0.981	100	0.14
2.426-2.544	0.207	88	0.173	1665	0.175	1757	0.972	0.981	99.7723	0.147
2.544-2.681	0.23	84	0.182	1607	0.185	1696	0.966	0.979	99.7052	0.153
2.681-2.843	0.184	80	0.178	1518	0.178	1601	0.977	0.98	99.8126	0.156
2.843-3.039	0.25	77	0.205	1456	0.207	1540	0.96	0.974	99.5455	0.179
3.039-3.281	0.248	70	0.188	1338	0.191	1412	0.961	0.979	99.7167	0.17
3.281-3.593	0.184	65	0.177	1228	0.177	1300	0.98	0.982	99.4615	0.164
3.593-4.014	0.161	60	0.154	1134	0.154	1198	0.983	0.987	99.6661	0.152
4.014-4.63	0.174	53	0.125	1017	0.127	1072	0.985	0.992	99.8134	0.127
4.63-5.657	0.153	46	0.128	871	0.129	917	0.987	0.99	100	0.135
5.657-7.947	0.216	37	0.148	697	0.151	734	0.981	0.988	100	0.155
7.947-48.66	0.191	23	0.145	433	0.147	456	0.986	0.987	100	0.166

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