PDB-8pi1: Bicyclic INCYPRO Pseudomonas fluorescens esterase

ID or keywords:

Entry

Database: PDB / ID: 8pi1

Title

Bicyclic INCYPRO Pseudomonas fluorescens esterase

Components

Arylesterase

Keywords

HYDROLASE / stabilization / cyclization / trimer / multimer / esterase

Function / homology

Function and homology information

arylesterase / Oxidoreductases / arylesterase activity / peroxidase activity
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Kiehstaller, S. / Pearce, N.M. / Grossmann, T.N. / Hennig, S.

Funding support

European Union,

Netherlands, 2items

Citation

Journal: Chem / Year: 2024
Title: Covalent bicyclization of protein complexes yields durable quaternary structures.
Authors: Hutchins, G.H. / Kiehstaller, S. / Poc, P. / Lewis, A.H. / Oh, J. / Sadighi, R. / Pearce, N.M. / Ibrahim, M. / Drienovska, I. / Rijs, A.M. / Neubacher, S. / Hennig, S. / Grossmann, T.N.

History

Deposition	Jun 20, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Database references / Derived calculations Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_gen 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	Feb 21, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Nov 6, 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	8pi1.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb8pi1.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	8pi1.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/pi/8pi1 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/8pi1	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	#165 - Sep 2013 Designed Protein Cages similarity (3) #220 - Apr 2018 Dehalogenases similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Arylesterase

B: Arylesterase

C: Arylesterase

D: Arylesterase

E: Arylesterase

F: Arylesterase

G: Arylesterase

H: Arylesterase

I: Arylesterase

J: Arylesterase

K: Arylesterase

L: Arylesterase

M: Arylesterase

N: Arylesterase

O: Arylesterase

hetero molecules

476 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Arylesterase

B: Arylesterase

C: Arylesterase

hetero molecules

defined by author
Evidence: mass spectrometry
95 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Arylesterase

E: Arylesterase

F: Arylesterase

hetero molecules

defined by author
95.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Arylesterase

H: Arylesterase

I: Arylesterase

hetero molecules

defined by author
95 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Arylesterase

K: Arylesterase

L: Arylesterase

hetero molecules

defined by author
95.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: Arylesterase

N: Arylesterase

O: Arylesterase

hetero molecules

defined by author
95.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	254.800, 146.250, 154.590
Angle α, β, γ (deg.)	90.00, 122.63, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Arylesterase / Aryl-ester hydrolase / Carboxylic acid perhydrolase / PFE / Putative bromoperoxidase Mass: 31075.201 Da / Num. of mol.: 15 / Mutation: T3C, Q174C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: estF / Production host: Escherichia coli (E. coli) / References: UniProt: P22862, arylesterase, Oxidoreductases
#2: Chemical	ChemComp-ZIZ / N-[2-[3,5-bis[2-(2-iodanylethanoylamino)ethanoyl]-1,3,5-triazinan-1-yl]-2-oxidanylidene-ethyl]-2-iodanyl-ethanamide Mass: 762.077 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₅H₂₁I₃N₆O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.6 Å³/Da / Density % sol: 52.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10 / Details: 100 mM CHES pH10 25 % (w/v) PEG3000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.5→99 Å / Num. obs: 164678 / % possible obs: 99.8 % / Redundancy: 14.1 % / CC_1/2: 0.997 / Net I/σ(I): 8.88
Reflection shell	Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 1.12 / Num. unique obs: 18210 / CC_1/2: 0.521 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
REFMAC	5.8.0411	refinement
PDB-REDO		refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→77.72 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.948 / SU B: 26.535 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22349	8234	5 %	RANDOM
R_work	0.18213	-	-	-
obs	0.1842	156444	99.99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 70.412 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	-0 Å²	0.26 Å²
2-	-	1.19 Å²	-0 Å²
3-	-	-	-0.79 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→77.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31861	0	420	533	32814

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	33108
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.868	1.646	44868
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.476	5	4082
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.894	5	240
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.101	10	5240
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	4859
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	25354
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.226	4.179	16355
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.003	7.517	20428
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.781	4.342	16753
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	4.596	42.9	48814
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.406	607	-
R_work	0.411	11536	-
obs	-	-	99.99 %

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	1.5563	-0.3075	-0.0944	2.0168	0.685	2.1183	-0.1355	-0.1151	-0.181	0.0567	0.1617	-0.2913	0.1902	0.4411	-0.0262	0.0842	0.0737	0.0673	0.3528	-0.0287	0.3182	90.1493	14.2755	-17.0872
2	0.9482	0.0679	0.1593	1.585	0.0578	1.7735	-0.1143	0.1052	0.0593	-0.1835	0.0164	0.0868	-0.128	0.0506	0.0979	0.0624	-0.0567	-0.0022	0.0905	0.0039	0.1968	65.293	41.636	-19.2375
3	1.5132	-0.2055	0.0299	1.5442	0.5713	1.975	-0.0757	0.3212	-0.0482	-0.2372	0.0658	-0.056	0.0234	0.1057	0.0099	0.1818	-0.1286	0.0893	0.288	-0.0457	0.1952	69.7014	17.0674	-47.3566
4	1.611	-0.2191	-0.2346	1.258	-0.1338	2.0425	-0.0511	0.1359	-0.0019	-0.1166	-0.0411	-0.0762	0.1224	0.0103	0.0923	0.0196	-0.0035	0.0198	0.0283	-0.013	0.1675	51.7889	-13.9046	-19.3878
5	1.6535	0.5165	0.152	1.3416	-0.3401	1.8481	-0.119	0.4006	0.0609	-0.2359	0.1186	0.0245	-0.008	-0.1806	0.0004	0.1342	-0.0843	-0.0207	0.3679	-0.0187	0.1347	29.4921	-5.4486	-47.7726
6	1.8853	-0.0147	0.4535	1.0749	-0.009	1.7278	-0.0175	-0.0543	-0.2177	0.032	-0.0161	0.1571	0.2593	-0.3189	0.0337	0.0955	-0.1469	0.0451	0.2434	-0.0685	0.217	15.8252	-22.3048	-17.4031
7	2.4033	0.6432	-0.0795	2.1523	-0.1476	1.8964	-0.1874	0.2426	0.5003	-0.1694	0.0465	-0.0037	-0.6449	0.0803	0.1409	0.5937	-0.0754	-0.0651	0.3063	0.1354	0.3769	20.8909	60.629	-17.2268
8	1.6541	0.3667	0.2726	1.4006	0.3327	1.9041	-0.0519	0.3196	-0.1009	-0.2183	0.0163	-0.0864	-0.1287	-0.0122	0.0356	0.0474	-0.0031	0.0457	0.2299	-0.0084	0.1391	10.1513	25.3316	-19.2593
9	1.2562	0.0338	-0.1979	2.0059	0.0442	1.1101	0.0104	0.5465	0.1299	-0.6203	-0.0871	-0.2576	-0.4485	0.2382	0.0768	0.6191	-0.1373	0.1578	0.7877	0.1385	0.296	29.1552	41.1748	-47.4119
10	2.2534	0.2963	0.2709	1.7736	0.2382	1.6666	0.0486	0.0048	0.2176	-0.0239	-0.068	0.0095	-0.1092	0.008	0.0195	0.0152	-0.014	0.0091	0.039	0.0075	0.1736	37.7158	38.1754	16.4147
11	1.8083	-0.1429	0.0712	1.7562	-0.2206	1.4118	0.0193	0.0245	-0.0261	0.0427	-0.0036	-0.25	0.1028	0.2152	-0.0157	0.0109	0.0102	-0.0063	0.0815	0.0097	0.169	62.8101	11.3203	16.5036
12	1.7934	-0.0361	-0.3776	1.648	0.1083	1.5469	-0.0529	0.0092	-0.094	0.0098	0.0546	0.0813	0.16	-0.1677	-0.0017	0.0281	-0.0417	0.0111	0.0763	-0.0065	0.0782	26.4864	3.1291	16.2628
13	2.9483	0.2232	0.3912	1.8844	0.8076	3.2681	-0.117	0.1055	0.2305	-0.131	0.0119	0.1963	-0.4183	-0.1311	0.1051	0.2498	-0.0883	-0.0268	0.2878	-0.0259	0.2874	32.5685	53.2135	76.1643
14	2.3521	0.3876	-0.0464	1.2243	0.5253	2.3388	-0.1348	0.3957	-0.5062	-0.0557	0.2	-0.4187	0.3187	0.8782	-0.0653	0.2872	-0.0481	0.0473	0.8441	-0.2083	0.4473	57.5864	33.3208	57.8379
15	2.715	0.7521	0.2255	1.3077	0.7948	2.9699	-0.0602	0.2982	-0.5777	0.1686	0.0549	0.0141	0.7379	-0.3256	0.0053	0.4287	-0.2481	0.0775	0.4813	-0.1288	0.4379	22.1967	22.1104	59.9171

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 402
2	X-RAY DIFFRACTION	2	B	2 - 277
3	X-RAY DIFFRACTION	3	C	2 - 272
4	X-RAY DIFFRACTION	4	D	2 - 402
5	X-RAY DIFFRACTION	5	E	2 - 274
6	X-RAY DIFFRACTION	6	F	2 - 273
7	X-RAY DIFFRACTION	7	G	2 - 402
8	X-RAY DIFFRACTION	8	H	2 - 276
9	X-RAY DIFFRACTION	9	I	2 - 273
10	X-RAY DIFFRACTION	10	J	2 - 402
11	X-RAY DIFFRACTION	11	K	2 - 273
12	X-RAY DIFFRACTION	12	L	2 - 272
13	X-RAY DIFFRACTION	13	M	2 - 402
14	X-RAY DIFFRACTION	14	N	2 - 272
15	X-RAY DIFFRACTION	15	O	2 - 272

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