PDB-5o2a: FolD Q98H

ID or keywords:

Entry

Database: PDB / ID: 5o2a

Title

FolD Q98H

Components

(Bifunctional protein FolD) 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 / L-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: 1.9 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: 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5o2a.cif.gz	644.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5o2a.ent.gz	546.2 KB	Display	PDB format
PDBx/mmJSON format	5o2a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5o2a_validation.pdf.gz	455.9 KB	Display	wwPDB validaton report
Full document	5o2a_full_validation.pdf.gz	465.9 KB	Display
Data in XML	5o2a_validation.xml.gz	50 KB	Display
Data in CIF	5o2a_validation.cif.gz	73.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o2/5o2a ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o2a	HTTPS FTP

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Related structure data

Related structure data	5o22C 5o28C 1diaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o28-2 5o28-1 1i7n-d 5o22-1 5o22-2 3ngl-d 5jaj-d 6qic-4 3l07-d 6qic-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

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

1

A: Bifunctional protein FolD

B: Bifunctional protein FolD

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

2

C: Bifunctional protein FolD

D: Bifunctional protein FolD

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

Unit cell

Length a, b, c (Å)	100.106, 79.393, 101.776
Angle α, β, γ (deg.)	90.00, 113.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Bifunctional protein FolD Mass: 31199.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) 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: 31199.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) 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: 31172.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) 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: 31145.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: folD, ads, b0529, JW0518 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24186, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.97 Å³/Da / Density % sol: 58.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 Ammonium Sulfate, Bis-Tris pH 6.0 and 25 % PEG 3350

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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: Mar 17, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 1.9→46.56 Å / Num. obs: 113661 / % possible obs: 98.79 % / Redundancy: 9.7 % / R_merge(I) obs: 0.061 / Net I/σ(I): 22.1
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 4.4 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DIA

1dia

Resolution: 1.9→46.562 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1812	5717	5.03 %
R_work	0.1658	-	-
obs	0.1666	113623	98.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→46.562 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8614	0	0	876	9490

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	8815
X-RAY DIFFRACTION	f_angle_d	1.102	12018
X-RAY DIFFRACTION	f_dihedral_angle_d	10.648	5377
X-RAY DIFFRACTION	f_chiral_restr	0.087	1437
X-RAY DIFFRACTION	f_plane_restr	0.007	1572

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 (%)
1.9-1.9216	0.2607	204	0.2336	3554	X-RAY DIFFRACTION	99
1.9216-1.9442	0.2052	164	0.2085	3625	X-RAY DIFFRACTION	99
1.9442-1.9679	0.2181	209	0.1992	3589	X-RAY DIFFRACTION	99
1.9679-1.9928	0.2169	175	0.1909	3575	X-RAY DIFFRACTION	99
1.9928-2.019	0.1919	203	0.1818	3585	X-RAY DIFFRACTION	99
2.019-2.0467	0.2147	200	0.1769	3588	X-RAY DIFFRACTION	100
2.0467-2.0759	0.2075	193	0.1775	3640	X-RAY DIFFRACTION	100
2.0759-2.1069	0.1927	202	0.1707	3551	X-RAY DIFFRACTION	100
2.1069-2.1399	0.1797	173	0.1683	3639	X-RAY DIFFRACTION	100
2.1399-2.1749	0.184	225	0.1633	3578	X-RAY DIFFRACTION	100
2.1749-2.2124	0.1757	179	0.1626	3623	X-RAY DIFFRACTION	99
2.2124-2.2527	0.1984	214	0.1652	3596	X-RAY DIFFRACTION	99
2.2527-2.296	0.1622	213	0.1656	3552	X-RAY DIFFRACTION	99
2.296-2.3429	0.1809	209	0.1581	3481	X-RAY DIFFRACTION	96
2.3429-2.3938	0.185	206	0.1619	3391	X-RAY DIFFRACTION	94
2.3938-2.4495	0.1755	199	0.1576	3219	X-RAY DIFFRACTION	90
2.4495-2.5107	0.1797	162	0.1579	3443	X-RAY DIFFRACTION	94
2.5107-2.5786	0.1925	208	0.162	3604	X-RAY DIFFRACTION	100
2.5786-2.6545	0.199	186	0.1703	3642	X-RAY DIFFRACTION	100
2.6545-2.7402	0.1885	186	0.1708	3618	X-RAY DIFFRACTION	100
2.7402-2.8381	0.1801	174	0.1731	3701	X-RAY DIFFRACTION	100
2.8381-2.9517	0.2091	182	0.167	3649	X-RAY DIFFRACTION	100
2.9517-3.086	0.2032	176	0.1684	3666	X-RAY DIFFRACTION	100
3.086-3.2487	0.1842	155	0.1697	3662	X-RAY DIFFRACTION	100
3.2487-3.4521	0.1641	168	0.1669	3715	X-RAY DIFFRACTION	100
3.4521-3.7186	0.1795	206	0.1575	3601	X-RAY DIFFRACTION	100
3.7186-4.0926	0.1735	152	0.1519	3722	X-RAY DIFFRACTION	100
4.0926-4.6843	0.1361	202	0.1361	3667	X-RAY DIFFRACTION	100
4.6843-5.8999	0.1593	195	0.1658	3696	X-RAY DIFFRACTION	100
5.8999-46.5755	0.2064	197	0.188	3734	X-RAY DIFFRACTION	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	1.5438	0.6016	-0.9221	1.6457	0.5331	1.0348	-0.0817	0.1118	-0.0174	-0.1373	0.089	-0.058	0.0127	0.0052	-0.001	0.1886	-0.0108	-0.0405	0.2069	-0.0179	0.2109	51.989	-22.745	99.1587
2	2.0346	-2.3828	0.8383	9.764	-2.5532	1.4982	-0.195	0.172	0.474	-0.1531	0.0153	0.105	-0.472	-0.1595	0.2545	0.4136	0.0125	-0.0841	0.3663	0.0394	0.3817	42.3706	-14.6174	97.0558
3	1.2937	0.2048	-0.1236	2.6596	1.011	1.2739	0.0081	-0.0832	0.2538	0.0485	0.0499	0.2673	-0.0754	0.1134	-0.0622	0.2033	-0.0162	0.0048	0.2261	-0.0245	0.258	49.5571	-6.7367	109.9288
4	1.0727	0.0877	-0.2249	1.7481	-0.0009	0.9468	-0.0447	0.0404	-0.0705	-0.0527	-0.0082	-0.1085	0.0734	-0.0561	0.057	0.1886	-0.0033	-0.0209	0.2082	-0.0306	0.2435	70.0529	-7.2727	91.9061
5	2.7653	-0.4149	0.7795	2.6523	-0.9413	2.7712	0.0355	0.2973	-0.1109	-0.3514	0.0006	0.276	0.0036	-0.4478	-0.0561	0.3197	-0.0089	-0.0499	0.3415	-0.0728	0.2848	63.5974	-7.7152	79.7146
6	2.0026	0.3749	-1.4656	0.9608	0.022	2.3392	-0.0545	0.0739	-0.1193	-0.1464	0.062	-0.0517	0.0513	-0.0351	0.0098	0.2288	-0.0157	-0.0358	0.187	-0.0561	0.2763	60.0065	-17.509	94.7466
7	5.1298	-1.289	-3.7727	0.9962	1.1612	4.1477	0.2696	-0.1154	0.2634	0.0865	0.0288	-0.0755	-0.8175	0.1575	-0.3322	0.4423	-0.0438	0.0586	0.2906	-0.065	0.284	79.0361	20.9603	116.9158
8	0.9109	0.9565	-0.3638	1.1254	0.0644	1.5025	0.0498	-0.0525	0.0419	0.5316	-0.1219	0.059	0.0575	-0.0384	0.0363	0.4082	-0.018	0.0272	0.3475	-0.0708	0.1884	71.0726	7.7079	131.1375
9	4.9019	-4.2085	1.7993	3.7438	-1.9902	2.1062	-0.2865	-0.2165	-0.0401	0.4754	0.2434	-0.4001	0.125	0.3487	0.1251	0.4457	-0.0033	0.0295	0.5191	-0.0622	0.3492	81.0075	8.004	129.8226
10	1.2155	0.535	0.5338	1.681	-0.2594	2.3314	0.1684	-0.1489	-0.1829	0.3117	-0.0093	-0.0669	0.4991	-0.1155	-0.1654	0.4797	-0.0361	0.0053	0.3853	-0.0496	0.2462	68.5236	-2.5167	130.5905
11	1.7337	0.8047	-0.6247	1.8545	-0.1149	5.0398	0.0857	0.1288	0.0429	0.0485	0.0269	-0.0037	0.1859	-0.0798	-0.1246	0.2348	-0.0472	0.0136	0.3343	-0.0698	0.2418	64.9462	2.7851	114.1772
12	0.8711	0.5525	0.0046	1.2548	0.6579	1.5685	0.0717	-0.0477	0.1435	0.0892	0.0269	0.0767	-0.1448	0.057	-0.0697	0.2156	-0.0051	0.0244	0.2284	-0.0459	0.2726	78.129	9.1088	104.3901
13	1.4506	0.1966	0.5635	1.154	0.0004	0.6731	-0.0047	0.19	-0.2648	0.0086	0.0032	-0.0343	0.0828	0.1176	0.0011	0.1999	0.0171	-0.0052	0.2476	-0.0577	0.2655	82.5113	-0.8142	100.0807
14	3.2457	0.1013	0.6291	1.6894	0.8957	0.9947	-0.0027	-0.2497	-0.1551	0.2553	-0.0551	-0.3105	0.0271	0.2954	0.0145	0.2242	0.0083	-0.0523	0.3043	-0.0336	0.2955	93.2364	4.2137	106.9031
15	1.9489	0.5335	-0.801	0.5897	-0.5025	1.8862	0.0215	-0.09	0.0931	0.198	-0.0161	0.0377	-0.1371	0.0447	-0.0166	0.2954	-0.0357	0.0023	0.2555	-0.0628	0.2496	79.8095	12.0138	112.7765
16	1.0952	0.2629	0.4921	1.4414	0.185	0.9559	-0.0894	-0.0217	0.3663	0.0102	-0.0711	-0.107	-0.228	-0.0317	0.1571	0.2565	0.009	-0.0003	0.2163	0.0122	0.3015	118.8128	-3.8599	102.4527
17	0.4135	-0.912	-0.7153	1.8821	1.4709	1.1243	0.0309	0.0159	0.0744	-0.2297	-0.0911	-0.1081	-0.0066	0.0335	-0.0655	0.4864	0.0541	-0.007	0.5921	0.0174	0.62	129.1328	-14.7924	97.8509
18	1.881	-0.802	-0.4971	1.1715	-0.2227	0.6586	-0.1007	-0.1977	-0.055	0.0776	0.0562	-0.0756	0.0602	0.0174	0.0562	0.2375	-0.0169	-0.0225	0.2649	0.0107	0.211	123.9601	-21.1779	111.5278
19	1.4743	0.2824	-0.3074	1.6136	0.074	1.0812	0.0297	0.0899	-0.0222	-0.0958	-0.0988	0.1674	0.0827	-0.059	0.0782	0.2044	0.0275	-0.0198	0.2248	-0.0173	0.2392	102.1599	-20.7659	94.0142
20	2.8601	-0.8402	-0.1295	1.2678	-0.1662	0.984	0.2661	0.5786	0.2204	-0.4094	-0.2585	-0.003	-0.0296	-0.0856	0.006	0.3013	0.0684	-0.0131	0.2971	0.0286	0.2475	108.1898	-16.35	82.3351
21	1.9328	-0.0789	0.7718	1.6067	-0.2111	4.357	0.1009	-0.1348	0.1912	0.1852	-0.1151	0.1043	-0.29	-0.0957	0.1308	0.2368	-0.0187	-0.0033	0.2099	-0.0102	0.3197	117.5841	-8.8896	108.7502
22	1.168	0.1644	0.6755	1.3938	0.3967	1.606	-0.1072	-0.1466	-0.1695	0.3029	0.0185	0.132	0.4631	-0.149	0.0573	0.4853	-0.0461	0.0506	0.3663	0.0795	0.3179	97.4029	-42.4409	129.1122
23	1.0376	0.3633	-0.1614	1.1008	-0.5269	2.7102	-0.026	-0.1361	-0.0037	0.2196	-0.0182	0.0176	-0.3764	0.1646	0.0084	0.3646	-0.005	0.0157	0.3093	0.0489	0.2256	108.1264	-27.8819	128.427
24	0.9901	0.0722	0.0428	2.7344	-0.8686	1.5876	0.0225	-0.0982	-0.0146	0.1627	0.0056	0.442	0.0962	-0.1713	0.0152	0.2712	-0.0392	0.0414	0.284	-0.024	0.339	88.675	-32.0302	108.4919
25	1.6472	0.542	1.0542	1.4339	0.3646	2.3115	0.0084	-0.1654	-0.1074	0.2525	-0.0352	0.3098	0.3286	-0.1603	-0.0243	0.4309	-0.0781	0.0937	0.2815	0.0585	0.3427	93.8962	-40.5368	117.7048

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 44 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 140 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 141 through 217 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 218 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 286 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 28 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 29 through 44 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 45 through 61 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 62 through 113 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 114 through 140 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 141 through 171 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 172 through 217 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 218 through 245 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 246 through 285 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 2 through 41 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 42 through 60 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 61 through 140 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 141 through 234 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 235 through 263 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 264 through 285 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1 through 61 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 62 through 140 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 141 through 245 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 246 through 285 )

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