PDB-5o22: E. coli FolD in complex with carolacton

ID or keywords:

Entry

Database: PDB / ID: 5o22

Title

E. coli FolD in complex with carolacton

Components

(Bifunctional protein ...

) x 4

Keywords

OXIDOREDUCTASE / carolacton / FolD /

natural product /

inhibitor

Function / homology

Function and homology information

methylenetetrahydrofolate dehydrogenase (NADP+) /

methenyltetrahydrofolate cyclohydrolase /

methenyltetrahydrofolate cyclohydrolase activity /

methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / protein homodimerization activity /

cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: Nat Commun / Year: 2017
Title: The natural product carolacton inhibits folate-dependent C1 metabolism by targeting FolD/MTHFD.
Authors: Fu, C. / Sikandar, A. / Donner, J. / Zaburannyi, N. / Herrmann, J. / Reck, M. / Wagner-Dobler, I. / Koehnke, J. / Muller, R.

History

Deposition	May 19, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5o22.cif.gz	642.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5o22.ent.gz	542.6 KB	Display	PDB format
PDBx/mmJSON format	5o22.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/o2/5o22 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o22	HTTPS FTP

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Related structure data

Related structure data	5o28C 5o2aC 1diaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o28-2 2p0a-d 5o2a-1 4gua-1 3zwm-2 1xet-2 3ngl-d 3l07-d 7cj3-d 5o28-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Bifunctional protein FolD

B: Bifunctional protein FolD

C: Bifunctional protein FolD

D: Bifunctional protein FolD

hetero molecules

127 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bifunctional protein FolD

B: Bifunctional protein FolD

hetero molecules

defined by author&software
63.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Bifunctional protein FolD

D: Bifunctional protein FolD

hetero molecules

defined by author&software
63.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.640, 81.016, 100.935
Angle α, β, γ (deg.)	90.00, 112.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Bifunctional protein ... , 4 types, 4 molecules ABCD

#1: Protein	Bifunctional protein FolD / Mass: 31189.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Lysines reductively methylated Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folD, ads, b0529, JW0518 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24186, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Protein	Bifunctional protein FolD / Mass: 31216.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folD, ads, b0529, JW0518 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24186, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#3: Protein	Bifunctional protein FolD / Mass: 31162.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folD, ads, b0529, JW0518 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24186, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#4: Protein	Bifunctional protein FolD / Mass: 31135.725 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folD, ads, b0529, JW0518 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24186, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase

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Non-polymers , 2 types, 706 molecules

#5: Chemical	ChemComp-C3R / Carolacton Mass: 468.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₅H₄₀O₈
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 6.5 and 30 % (w/v) PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.1→92.95 Å / Num. obs: 86516 / % possible obs: 98.9 % / Redundancy: 4.4 % / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DIA

1dia

Resolution: 2.1→45.876 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2056	4258	4.98 %
R_work	0.1748	-	-
obs	0.1763	85476	98.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→45.876 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8453	0	132	702	9287

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8766
X-RAY DIFFRACTION	f_angle_d	0.712	11939
X-RAY DIFFRACTION	f_dihedral_angle_d	12.168	5286
X-RAY DIFFRACTION	f_chiral_restr	0.05	1445
X-RAY DIFFRACTION	f_plane_restr	0.004	1548

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 (%)
2.1-2.1239	0.2678	139	0.2533	2755	X-RAY DIFFRACTION	100
2.1239-2.1489	0.3008	131	0.2504	2728	X-RAY DIFFRACTION	100
2.1489-2.1751	0.2841	154	0.2459	2697	X-RAY DIFFRACTION	100
2.1751-2.2026	0.3127	122	0.2408	2714	X-RAY DIFFRACTION	100
2.2026-2.2316	0.2864	120	0.2289	2731	X-RAY DIFFRACTION	100
2.2316-2.2621	0.2511	151	0.2184	2745	X-RAY DIFFRACTION	100
2.2621-2.2945	0.2416	136	0.2139	2720	X-RAY DIFFRACTION	100
2.2945-2.3287	0.2402	154	0.2091	2675	X-RAY DIFFRACTION	100
2.3287-2.3651	0.2474	149	0.2104	2724	X-RAY DIFFRACTION	100
2.3651-2.4039	0.2327	121	0.2017	2744	X-RAY DIFFRACTION	100
2.4039-2.4453	0.2574	149	0.1928	2696	X-RAY DIFFRACTION	99
2.4453-2.4898	0.2361	136	0.1959	2668	X-RAY DIFFRACTION	99
2.4898-2.5377	0.2271	159	0.1855	2699	X-RAY DIFFRACTION	98
2.5377-2.5895	0.1951	154	0.1802	2692	X-RAY DIFFRACTION	99
2.5895-2.6458	0.232	153	0.1899	2673	X-RAY DIFFRACTION	99
2.6458-2.7073	0.2436	146	0.1936	2673	X-RAY DIFFRACTION	99
2.7073-2.775	0.2145	136	0.1874	2680	X-RAY DIFFRACTION	98
2.775-2.85	0.2303	122	0.183	2691	X-RAY DIFFRACTION	97
2.85-2.9339	0.2058	126	0.178	2639	X-RAY DIFFRACTION	96
2.9339-3.0285	0.1935	125	0.1762	2466	X-RAY DIFFRACTION	91
3.0285-3.1368	0.2041	128	0.1746	2612	X-RAY DIFFRACTION	94
3.1368-3.2623	0.2159	143	0.1792	2726	X-RAY DIFFRACTION	100
3.2623-3.4107	0.1987	144	0.17	2720	X-RAY DIFFRACTION	100
3.4107-3.5905	0.185	183	0.158	2717	X-RAY DIFFRACTION	100
3.5905-3.8153	0.1924	148	0.1512	2756	X-RAY DIFFRACTION	100
3.8153-4.1098	0.186	136	0.145	2735	X-RAY DIFFRACTION	100
4.1098-4.523	0.1533	142	0.131	2775	X-RAY DIFFRACTION	100
4.523-5.1767	0.1592	173	0.1321	2733	X-RAY DIFFRACTION	100
5.1767-6.5192	0.2223	126	0.1754	2802	X-RAY DIFFRACTION	100
6.5192-45.8864	0.1863	152	0.1818	2832	X-RAY DIFFRACTION	100

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	1.9324	0.2896	0.2336	4.0289	0.4497	2.2714	0.2054	0.1286	-0.048	-0.3177	-0.5185	0.4063	0.101	-0.2597	0.2681	0.2134	0.0755	-0.0321	0.3271	-0.0868	0.2667	-6.8325	-7.0702	1.1977
2	2.0926	-0.646	0.1895	2.2445	0.4016	0.653	0.1323	0.3482	0.3692	-0.3641	-0.4028	-0.0521	-0.1527	-0.0599	0.1723	0.2353	0.072	0.0371	0.2757	0.0886	0.2867	3.2144	0.9386	0.9516
3	2.4842	0.1917	1.4654	1.7788	1.1101	2.5159	-0.0901	0.0513	-0.7204	0.3252	-0.0786	0.1761	0.9147	-0.4071	0.1404	0.7369	-0.1741	0.2359	0.414	0.0339	0.582	-9.3681	-31.9299	33.2533
4	1.7736	0.519	0.0729	6.7381	0.4711	4.197	0.0367	-0.4085	-0.1603	0.175	0.0358	0.2885	0.1525	-0.2223	-0.0508	0.4729	-0.0032	0.0286	0.5212	0.1219	0.2973	-2.3268	-17.899	42.9185
5	9.2433	-1.9729	-3.2499	5.7067	-0.1034	7.8983	0.4535	-0.3834	0.6503	-0.1196	-0.1129	0.3236	-1.1358	-0.353	-0.3196	0.5962	0.1058	0.0745	0.3137	0.0176	0.2744	-3.9009	-5.7286	37.2887
6	7.4444	-0.3999	-0.4178	7.7365	-2.9338	6.2162	-0.1391	0.1579	-0.4974	0.1295	-0.007	0.1826	0.3314	-0.2881	0.092	0.3225	-0.1095	0.0957	0.2457	-0.0279	0.2505	0.3909	-17.4127	24.683
7	1.8789	-0.1066	-0.3791	2.4105	-0.3632	1.0565	0.0346	0.143	-0.2851	0.3289	-0.3337	0.7295	0.3893	-0.5053	0.1886	0.3352	-0.1767	0.1411	0.5541	-0.2509	0.522	-18.9327	-18.7955	15.0831
8	3.122	1.7077	1.2465	1.3749	0.8973	2.4225	-0.0015	-0.1433	-0.3399	0.3481	-0.2103	0.3846	0.5452	-0.4652	0.0932	0.6532	-0.222	0.2565	0.4019	-0.1257	0.6376	-14.005	-27.0281	25.1443
9	1.6836	0.0464	-0.7181	1.2141	1.0235	1.371	0.0652	0.0702	0.159	-0.1676	0.0603	0.1702	-0.0674	-0.0766	-0.1401	0.2136	-0.0245	-0.0405	0.1936	0.0306	0.2906	-61.0516	-4.4289	6.7832
10	4.3879	-0.3677	0.0896	7.2391	0.52	4.2413	-0.0635	-0.1462	0.5764	-0.0333	-0.0334	0.411	-0.2114	-0.1712	0.1215	0.2093	-0.0091	0.0129	0.2706	-0.0315	0.3905	-63.5814	10.2366	17.8521
11	1.962	2.5197	-1.8167	5.9385	0.3861	5.9299	0.1487	-0.1185	0.221	-0.032	0.1216	-0.2212	0.0151	0.2391	-0.254	0.1736	-0.022	-0.0255	0.22	-0.0721	0.2171	-48.2453	5.2941	16.4051
12	2.2008	1.109	-0.925	2.1932	-0.3734	0.7415	0.0105	0.1449	-0.0704	-0.2084	0.0013	0.0243	0.0742	-0.0303	-0.0213	0.2344	0.0142	-0.051	0.2029	-0.0291	0.2199	-43.0186	4.4725	-2.8077
13	3.7236	-1.3919	-4.8976	1.0832	1.6237	6.4602	0.349	-0.0629	0.6422	-0.0367	0.0606	-0.1942	-0.8636	0.1041	-0.5215	0.4353	-0.0779	0.0428	0.2746	-0.12	0.3204	-29.9996	35.4436	23.7404
14	1.595	1.0343	-0.5282	0.9001	-0.7596	1.6738	0.3946	-0.2961	-0.0435	0.1415	-0.2412	-0.0823	0.2366	0.4502	-0.1067	0.5399	-0.0144	-0.0232	0.5198	-0.1628	0.288	-33.7122	20.8497	38.2084
15	3.9603	-0.3802	1.0354	6.4561	0.0129	4.642	0.1977	-0.4511	-0.2788	0.3785	0.0936	-0.1158	0.5633	-0.1557	-0.2688	0.4364	-0.0917	0.0019	0.3607	-0.0215	0.2606	-41.4056	10.6192	35.5434
16	4.8671	0.3185	2.7508	4.4819	0.0792	2.0555	0.1822	-0.1178	0.0823	0.1052	0.0302	0.1392	0.0233	0.1297	-0.1242	0.2073	-0.0521	0.0412	0.2365	-0.0643	0.2287	-43.5354	17.2248	20.662
17	1.9629	0.3239	-0.072	2.9137	0.5058	2.171	0.0093	0.0588	-0.1138	0.0664	0.1159	-0.2328	-0.011	0.3622	-0.116	0.1942	-0.0132	-0.0069	0.2777	-0.0768	0.2133	-23.6619	19.0266	9.8103
18	2.0235	0.6644	-2.246	2.9517	0.2666	3.6803	0.3396	-0.2346	0.4441	0.0673	-0.1248	0.2224	-0.3411	-0.1824	-0.2328	0.3229	-0.019	0.0393	0.2625	-0.0865	0.2293	-38.5134	26.8832	26.097
19	3.1862	-1.0813	1.71	1.5331	-0.5258	1.403	0.0789	0.1078	0.7211	-0.0752	-0.2376	-0.2319	-0.2062	-0.0415	0.1687	0.2643	0.0041	0.005	0.2367	0.0804	0.3713	9.764	10.1256	9.0621
20	2.1106	-2.456	0.5154	2.9658	-0.9061	0.9911	0.3116	0.4942	0.5824	-0.3068	-0.4354	0.0998	0.2267	-0.0619	0.2046	0.7166	-0.0094	0.0299	0.7906	-0.026	0.8812	21.4724	-3.4579	2.503
21	3.87	-1.4212	-0.4954	1.3854	0.2845	1.3167	-0.2115	0.008	0.1293	0.1884	0.0718	-0.1252	0.0875	-0.0433	0.1462	0.2097	-0.0394	-0.0318	0.1773	0.0058	0.1692	15.1717	-6.0936	17.6845

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 141 through 234 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 235 through 285 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 1 through 50 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 51 through 97 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 98 through 113 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 114 through 140 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 141 through 245 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 246 through 285 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 2 through 75 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 76 through 113 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 114 through 140 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 141 through 286 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 28 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 29 through 75 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 76 through 113 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 114 through 140 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 141 through 262 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 263 through 284 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 2 through 41 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 42 through 56 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 57 through 140 )

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Bifunctional protein ... , 4 types, 4 molecules ABCD

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Non-polymers , 2 types, 706 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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-Related structure data

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-Bifunctional protein ... , 4 types, 4 molecules ABCD

-Non-polymers , 2 types, 706 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

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Bifunctional protein ... , 4 types, 4 molecules ABCD

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Non-polymers , 2 types, 706 molecules

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

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Jul 12, 2017. Major update of PDB

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Yorodumi