PDB-8cjh: Architecture of a PKS-NRPS hybrid megaenzyme involved in the bios...

ID or keywords:

Entry

Database: PDB / ID: 8cjh

Title

Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin

Components

Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

Keywords

BIOSYNTHETIC PROTEIN / polyketide Synthase / ketosynthase domain / Acyltransferase domain / Acyl Carrier Protein domain

Function / homology

Function and homology information

small molecule metabolic process / ligase activity, forming carbon-sulfur bonds / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / acyltransferase activity / phosphopantetheine binding / oxidoreductase activity / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.982 Å

Authors

Bonhomme, S. / Dessen, A. / Macheboeuf, P.

Funding support

France, 2items

Citation

Journal: Structure / Year: 2023
Title: Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin.
Authors: Bonhomme, S. / Contreras-Martel, C. / Dessen, A. / Macheboeuf, P.

History

Deposition	Feb 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: Database references / Refinement description / Category: citation / struct_ncs_dom / struct_ncs_dom_lim Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.end_auth_asym_id
Revision 1.2	Jun 19, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cjh.cif.gz	1.4 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/8cjh ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cjh	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	#90 - Jun 2007 Fatty Acid Synthase similarity (11) #78 - Jun 2006 Luciferase similarity (4) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

B: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

C: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

D: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

E: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

F: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

513 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

B: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

E: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

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

2

C: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

D: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

F: Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK

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

Unit cell

Length a, b, c (Å)	187.643, 233.374, 256.598
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A
13	7	E
14	7	F

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
2	1	1	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
3	2	2	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
4	2	2	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
5	3	3	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
6	3	3	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
7	4	4	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
8	4	4	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
9	5	5	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
10	5	5	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
11	6	6	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
12	6	6	MET	MET	ARG	ARG	A	A	1 - 696	1 - 696
13	7	7	ASN	ASN	LEU	LEU	E	E	706 - 783	706 - 783
14	7	7	ASN	ASN	LEU	LEU	F	F	706 - 783	706 - 783

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14

#1: Protein	Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK / Putative hybrid non-ribosomal peptide-polyketide synthetase Mass: 85430.398 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Chains A,B,E form a dimer Chains C,D,F form a dimer Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clbK, E4T84_20075 / Production host: Escherichia coli (E. coli) / Variant (production host): BAP1 / References: UniProt: Q0P7K1

#1: Protein

Colibactin hybrid non-ribosomal peptide synthetase/type I polyketide synthase ClbK / Putative hybrid non-ribosomal peptide-polyketide synthetase

Mass: 85430.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Chains A,B,E form a dimer Chains C,D,F form a dimer
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: clbK, E4T84_20075 / Production host:

Escherichia coli (E. coli) / Variant (production host): BAP1 / References: UniProt: Q0P7K1

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 19 % PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9655 Å / Relative weight: 1
Reflection	Resolution: 2.98→49.395 Å / Num. obs: 114296 / % possible obs: 93.6 % / Redundancy: 2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.138 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.98→3.088 Å / R_merge(I) obs: 1.05 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5592 / CC_1/2: 0.522

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.982→49.395 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.896 / SU B: 53.214 / SU ML: 0.377 / Cross valid method: FREE R-VALUE / ESU R Free: 0.437
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2384	1940	2.478 %
R_work	0.2171	76349	-
all	0.218	-	-
obs	-	78289	68.481 %

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: 95.226 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.03 Å²	-0 Å²	0 Å²
2-	-	0.709 Å²	-0 Å²
3-	-	-	0.321 Å²

Refinement step

Cycle: LAST / Resolution: 2.982→49.395 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22022	0	0	0	22022

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	22482
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	21022
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.01	0.01	1726
X-RAY DIFFRACTION	r_angle_refined_deg	1.105	1.641	30616
X-RAY DIFFRACTION	r_angle_other_deg	0.393	1.564	48216
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.87	5	2882
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.011	5	146
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.367	10	3526
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.12	10	1010
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	3490
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	26930
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5230
X-RAY DIFFRACTION	r_nbd_refined	0.261	0.2	5333
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	21905
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	11402
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	11926
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	305
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.021	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.202	0.2	69
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	211
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.554	0.2	5
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.325	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	3.682	4.947	11558
X-RAY DIFFRACTION	r_mcbond_other	3.682	4.947	11558
X-RAY DIFFRACTION	r_mcangle_it	6.021	8.889	14430
X-RAY DIFFRACTION	r_mcangle_other	6.021	8.889	14431
X-RAY DIFFRACTION	r_scbond_it	3.944	5.277	10924
X-RAY DIFFRACTION	r_scbond_other	3.944	5.277	10925
X-RAY DIFFRACTION	r_scangle_it	6.466	9.557	16186
X-RAY DIFFRACTION	r_scangle_other	6.465	9.557	16187
X-RAY DIFFRACTION	r_lrange_it	9.202	49.442	26941
X-RAY DIFFRACTION	r_lrange_other	9.202	49.443	26942
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.037	0.05	23036
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.04	0.05	22993
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.036	0.05	23105
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.042	0.05	22942
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.038	0.05	22995
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.046	0.05	22888
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.023	0.05	2483

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.03654	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.03654	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04012	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.04012	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.03633	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.03633	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.04181	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.04181	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.03775	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.03775	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.04557	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.04557	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.023	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.023	0.05009

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
2.982-3.059	0.14	3	0.345	77	0.334	8383	0.924	0.918	0.9543	0.353
3.059-3.142	0.266	15	0.342	569	0.34	8091	0.96	0.918	7.2179	0.34
3.142-3.233	0.429	30	0.352	1295	0.354	7940	0.837	0.908	16.6877	0.353
3.233-3.332	0.313	54	0.332	2276	0.332	7704	0.931	0.92	30.244	0.324
3.332-3.441	0.348	98	0.306	3290	0.307	7445	0.919	0.936	45.5071	0.285
3.441-3.561	0.322	122	0.29	4596	0.29	7268	0.932	0.945	64.9147	0.265
3.561-3.695	0.27	138	0.279	5909	0.279	6975	0.952	0.949	86.6953	0.251
3.695-3.845	0.256	154	0.251	6208	0.251	6744	0.957	0.959	94.3357	0.22
3.845-4.015	0.235	165	0.232	6204	0.232	6454	0.959	0.964	98.683	0.201
4.015-4.209	0.249	132	0.219	6034	0.219	6179	0.962	0.968	99.7896	0.19
4.209-4.435	0.212	145	0.201	5748	0.201	5907	0.97	0.974	99.763	0.175
4.435-4.702	0.217	155	0.192	5423	0.192	5600	0.967	0.977	99.6071	0.167
4.702-5.023	0.2	115	0.197	5113	0.197	5243	0.972	0.975	99.7139	0.175
5.023-5.421	0.258	123	0.198	4779	0.199	4913	0.959	0.975	99.7761	0.174
5.421-5.931	0.242	114	0.21	4394	0.211	4523	0.961	0.972	99.6684	0.186
5.931-6.619	0.236	120	0.204	3995	0.205	4126	0.961	0.974	99.7334	0.183
6.619-7.62	0.215	97	0.187	3549	0.188	3670	0.973	0.978	99.346	0.173
7.62-9.278	0.16	63	0.169	3040	0.169	3139	0.984	0.982	98.8531	0.166
9.278-12.896	0.21	48	0.176	2394	0.177	2468	0.975	0.98	98.9465	0.184
12.896-49.395	0.3	49	0.278	1456	0.279	1519	0.934	0.951	99.0783	0.28

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	2.6158	-0.1685	-0.599	2.9604	0.1761	2.5056	-0.0736	-0.5231	0.2746	0.4252	-0.0216	-0.2424	-0.2851	0.0701	0.0951	0.3093	0.1892	-0.0413	0.2591	-0.0378	0.0759	-85.5228	39.0126	-13.4438
2	2.5407	2.0916	-0.5133	5.1328	-0.5777	2.2779	-0.0368	0.1192	-0.4524	-0.0039	0.0538	0.3128	0.7367	-0.4923	-0.0171	0.4245	0.0694	-0.001	0.4208	0.0505	0.3702	-83.076	-0.7694	-20.2679
3	2.0234	-0.3665	-0.4848	2.9086	0.0035	2.4668	-0.1289	0.0306	-0.0549	-0.1351	0.1755	0.1954	0.2251	-0.1732	-0.0466	0.1637	0.0506	-0.0037	0.0664	0.0215	0.0612	-104.4913	38.6931	-38.7593
4	4.0145	0.8397	-1.922	1.5464	-0.1674	3.5968	0.0457	-0.7999	-0.0764	0.5926	-0.0372	0.6075	0.0838	-0.409	-0.0085	0.5974	0.2184	0.1783	0.5147	0.1107	0.5299	-129.0745	60.9505	-15.5911
5	3.0825	-0.3986	0.1163	2.2248	-0.2573	2.283	0.0693	-0.2021	0.3449	0.1677	0.0287	0.0052	-0.0582	0.1956	-0.0979	0.1693	0.0883	0.0979	0.1309	-0.0295	0.1576	-126.3521	117.5849	-24.7321
6	1.5648	0.4178	-0.5153	2.8211	-1.9235	3.7356	-0.1508	0.4877	0.5977	-0.5608	0.089	-0.2593	-0.3485	0.1712	0.0618	0.6022	0.0583	0.1896	0.5169	0.0837	0.6764	-143.5934	145.9259	-47.9333
7	3.1574	-0.2688	0.2677	2.3973	-0.5445	2.3036	-0.0631	0.5317	0.0219	-0.3874	0.0749	0.2477	0.1102	-0.2794	-0.0118	0.3419	0.0847	0.0577	0.2043	0.0417	0.0713	-131.6568	98.4456	-49.5358
8	5.3677	2.3021	-0.7616	2.7155	-0.3906	2.3982	0.0824	0.0957	0.1315	0.013	0.0982	-0.6975	-0.3005	0.8492	-0.1806	0.4553	0.0544	0.0915	0.4339	-0.147	0.4954	-93.1109	87.8812	-43.6647
9	2.6738	-3.0767	-1.2558	3.977	1.3022	0.6422	-0.1834	-0.5867	0.473	0.9403	0.4345	-0.5168	-0.1562	0.2855	-0.2511	1.2323	-0.1899	-0.0315	1.2296	0.0972	1.2612	-68.2994	60.293	-71.1648
10	2.6505	-1.2498	1.0423	0.5969	-0.5065	0.4497	0.3575	0.3819	-0.3079	-0.2481	-0.1133	0.1468	0.229	-0.0507	-0.2442	1.4745	-0.2278	0.0363	1.4329	-0.1291	1.4866	-145.5759	97.4147	5.7679

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 424
2	X-RAY DIFFRACTION	2	ALL	A	425 - 696

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Assembly

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi