PDB-7qjr: Crystal structure of cutinase 1 from Thermobifida fusca DSM44342 (703)

ID or keywords:

Entry

Database: PDB / ID: 7qjr

Title

Crystal structure of cutinase 1 from Thermobifida fusca DSM44342 (703)

Components

Cutinase 1

Keywords

HYDROLASE / plastic degradation

Function / homology

Function and homology information

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

Biological species

Thermobifida fusca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.51 Å

Authors

Zahn, M. / Avilan, L. / Beckham, G.T. / McGeehan, J.E.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / ...

History

Deposition	Dec 17, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 28, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	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	7qjr.cif.gz	192.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7qjr.ent.gz	148.6 KB	Display	PDB format
PDBx/mmJSON format	7qjr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7qjr_validation.pdf.gz	674 KB	Display	wwPDB validaton report
Full document	7qjr_full_validation.pdf.gz	674 KB	Display
Data in XML	7qjr_validation.xml.gz	13.6 KB	Display
Data in CIF	7qjr_validation.cif.gz	20.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/7qjr ftp://data.pdbj.org/pub/pdb/validation_reports/qj/7qjr	HTTPS FTP

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Related structure data

Related structure data	7qjmC 7qjnC 7qjoC 7qjpC 7qjqC 7qjsC 7qjtC 4cg1S S: Starting model for refinement 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 (2)

Deposited unit

A: Cutinase 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	71.680, 71.680, 102.520
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Cutinase 1 Mass: 29601.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: cut1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9LVI0
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.57 Å³/Da / Density % sol: 52.11 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, hanging drop Details: 20 % PEG 3350, 0.02 M sodium / potassium phosphate, 0.1 M Bis-Tris propane pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 1.51→62.08 Å / Num. obs: 48462 / % possible obs: 100 % / Redundancy: 19.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.115 / R_pim(I) all: 0.027 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.51→1.54 Å / R_merge(I) obs: 3.682 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2368 / CC_1/2: 0.35 / R_pim(I) all: 0.852 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
xia2		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4CG1

4cg1

Resolution: 1.51→62.077 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.973 / SU B: 3.084 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1855	2307	4.765 %
R_work	0.1542	46109	-
all	0.156	-	-
obs	-	48416	99.996 %

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: 25.381 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.041 Å²	0.021 Å²	0 Å²
2-	-	0.041 Å²	-0 Å²
3-	-	-	-0.133 Å²

Refinement step

Cycle: LAST / Resolution: 1.51→62.077 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2018	0	10	222	2250

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.013	2112
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1957
X-RAY DIFFRACTION	r_angle_refined_deg	2.044	1.648	2886
X-RAY DIFFRACTION	r_angle_other_deg	1.614	1.571	4516
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.651	5	276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.004	20.455	110
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.068	15	322
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.457	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	283
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	2424
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	502
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	388
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	1884
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1065
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1056
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	154
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.108	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	18
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.19	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	1.617	2.045	1065
X-RAY DIFFRACTION	r_mcbond_other	1.608	2.041	1064
X-RAY DIFFRACTION	r_mcangle_it	2.431	3.062	1333
X-RAY DIFFRACTION	r_mcangle_other	2.43	3.065	1334
X-RAY DIFFRACTION	r_scbond_it	2.625	2.346	1047
X-RAY DIFFRACTION	r_scbond_other	2.627	2.35	1048
X-RAY DIFFRACTION	r_scangle_it	3.943	3.402	1546
X-RAY DIFFRACTION	r_scangle_other	3.941	3.405	1547
X-RAY DIFFRACTION	r_lrange_it	5.624	25.612	2380
X-RAY DIFFRACTION	r_lrange_other	5.516	24.891	2329

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
1.51-1.549	0.308	156	0.299	3358	0.3	3514	0.711	0.737	100	0.297
1.549-1.592	0.262	178	0.272	3271	0.271	3449	0.811	0.803	100	0.264
1.592-1.638	0.267	164	0.25	3175	0.251	3339	0.845	0.845	100	0.235
1.638-1.688	0.27	189	0.234	3091	0.236	3280	0.851	0.877	100	0.214
1.688-1.744	0.208	127	0.204	3024	0.204	3151	0.92	0.919	100	0.178
1.744-1.805	0.233	117	0.189	2954	0.191	3071	0.922	0.928	100	0.163
1.805-1.873	0.197	165	0.161	2807	0.162	2972	0.939	0.952	100	0.135
1.873-1.949	0.177	138	0.157	2678	0.158	2816	0.955	0.957	100	0.13
1.949-2.036	0.192	133	0.149	2624	0.151	2757	0.953	0.963	100	0.124
2.036-2.135	0.184	134	0.141	2492	0.143	2626	0.958	0.969	100	0.12
2.135-2.25	0.152	111	0.133	2374	0.134	2485	0.969	0.973	100	0.115
2.25-2.387	0.223	116	0.139	2255	0.143	2371	0.956	0.971	100	0.123
2.387-2.551	0.235	105	0.151	2152	0.155	2257	0.947	0.966	100	0.138
2.551-2.755	0.227	81	0.153	1987	0.156	2068	0.95	0.966	100	0.144
2.755-3.018	0.163	96	0.161	1824	0.161	1920	0.962	0.962	100	0.154
3.018-3.373	0.187	81	0.15	1677	0.152	1758	0.964	0.971	100	0.15
3.373-3.893	0.138	89	0.137	1466	0.137	1555	0.982	0.979	100	0.147
3.893-4.763	0.137	58	0.116	1282	0.117	1340	0.983	0.985	100	0.133
4.763-6.716	0.208	40	0.148	1014	0.15	1054	0.957	0.979	100	0.171
6.716-62.077	0.169	29	0.145	604	0.146	635	0.977	0.98	99.685	0.173

Refinement TLS params.

Method: refined / Origin x: -21.8316 Å / Origin y: -10.8902 Å / Origin z: -13.2095 Å

	11	12	13	21	22	23	31	32	33
T	0.0409 Å²	0.0219 Å²	-0.0119 Å²	-	0.0184 Å²	0.002 Å²	-	-	0.0187 Å²
L	0.2219 °²	-0.1699 °²	0.2782 °²	-	0.4891 °²	-0.2871 °²	-	-	0.613 °²
S	-0.0366 Å °	-0.0132 Å °	-0.0088 Å °	-0.0003 Å °	-0.0167 Å °	-0.0068 Å °	-0.0614 Å °	0.0153 Å °	0.0533 Å °

Refinement TLS group

Selection: ALL

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