PDB-5o28: E. coli FolD apo

ID or keywords:

Entry

Database: PDB / ID: 5o28

Title

E. coli FolD apo

Components

(Bifunctional protein FolD) x 3

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: 1.89 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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PDBx/mmCIF format	5o28.cif.gz	458.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5o28.ent.gz	376.3 KB	Display	PDB format
PDBx/mmJSON format	5o28.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5o28_validation.pdf.gz	453.3 KB	Display	wwPDB validaton report
Full document	5o28_full_validation.pdf.gz	464.5 KB	Display
Data in XML	5o28_validation.xml.gz	52.2 KB	Display
Data in CIF	5o28_validation.cif.gz	75.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o2/5o28 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o28	HTTPS FTP

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Related structure data

Related structure data	5o22C 5o2aC 1diaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o2a-2 5o2a-1 5o22-2 3l07-d 3ngl-d 1i7n-d 5u8o-2 1b0a-1 6qic-1 5jaj-d 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)	99.590, 79.840, 101.410
Angle α, β, γ (deg.)	90.00, 113.26, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Bifunctional protein FolD Mass: 31216.861 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: 31216.857 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: 31162.771 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) / Gene: folD, ads, b0529, JW0518 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24186, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1014 / 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: 58.57 %
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: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.89→36.14 Å / Num. obs: 116659 / % possible obs: 99.73 % / Redundancy: 6.7 % / R_merge(I) obs: 0.084 / Net I/σ(I): 17.9
Reflection shell	Resolution: 1.89→1.94 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.79 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9

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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: 1.89→36.14 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.44

	R_factor	Num. reflection	% reflection
R_free	0.2091	5747	4.93 %
R_work	0.1836	-	-
obs	0.1849	116659	99.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.89→36.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8617	0	0	1014	9631

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8790
X-RAY DIFFRACTION	f_angle_d	0.637	11978
X-RAY DIFFRACTION	f_dihedral_angle_d	12.29	5368
X-RAY DIFFRACTION	f_chiral_restr	0.047	1434
X-RAY DIFFRACTION	f_plane_restr	0.003	1564

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 (%)
1.89-1.9115	0.3854	185	0.3706	3715	X-RAY DIFFRACTION	99
1.9115-1.934	0.4053	193	0.3888	3582	X-RAY DIFFRACTION	98
1.934-1.9576	0.3013	184	0.2784	3695	X-RAY DIFFRACTION	100
1.9576-1.9823	0.2448	172	0.2421	3718	X-RAY DIFFRACTION	100
1.9823-2.0084	0.2757	219	0.2321	3641	X-RAY DIFFRACTION	100
2.0084-2.0359	0.2327	189	0.2261	3697	X-RAY DIFFRACTION	100
2.0359-2.065	0.3064	186	0.271	3656	X-RAY DIFFRACTION	99
2.065-2.0958	0.3211	197	0.2732	3630	X-RAY DIFFRACTION	99
2.0958-2.1286	0.2271	192	0.1977	3706	X-RAY DIFFRACTION	100
2.1286-2.1635	0.2451	203	0.1922	3703	X-RAY DIFFRACTION	100
2.1635-2.2008	0.2066	179	0.1894	3675	X-RAY DIFFRACTION	100
2.2008-2.2408	0.2459	211	0.2095	3657	X-RAY DIFFRACTION	100
2.2408-2.2839	0.2837	171	0.2437	3628	X-RAY DIFFRACTION	98
2.2839-2.3305	0.1996	169	0.1783	3689	X-RAY DIFFRACTION	100
2.3305-2.3812	0.2127	216	0.177	3678	X-RAY DIFFRACTION	100
2.3812-2.4365	0.1918	185	0.1717	3735	X-RAY DIFFRACTION	100
2.4365-2.4975	0.2068	205	0.1754	3670	X-RAY DIFFRACTION	100
2.4975-2.565	0.2063	165	0.1742	3716	X-RAY DIFFRACTION	100
2.565-2.6404	0.2144	173	0.1776	3730	X-RAY DIFFRACTION	100
2.6404-2.7256	0.2042	198	0.1811	3680	X-RAY DIFFRACTION	100
2.7256-2.823	0.1997	180	0.1675	3720	X-RAY DIFFRACTION	100
2.823-2.936	0.1963	176	0.1748	3740	X-RAY DIFFRACTION	100
2.936-3.0695	0.1867	191	0.1692	3708	X-RAY DIFFRACTION	100
3.0695-3.2313	0.1916	197	0.1685	3682	X-RAY DIFFRACTION	100
3.2313-3.4336	0.2059	216	0.1674	3694	X-RAY DIFFRACTION	100
3.4336-3.6985	0.1941	200	0.1619	3726	X-RAY DIFFRACTION	100
3.6985-4.0702	0.1669	204	0.1524	3704	X-RAY DIFFRACTION	100
4.0702-4.6582	0.1578	175	0.1328	3766	X-RAY DIFFRACTION	100
4.6582-5.8649	0.1676	208	0.1536	3755	X-RAY DIFFRACTION	100
5.8649-36.5959	0.1962	208	0.1833	3815	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	0.2671	0.1741	0.144	0.4242	0.0335	0.3338	0.0407	-0.0424	0.1371	-0.0761	-0.2552	0.2441	-0.0005	-0.0974	-0.3212	0.1405	0.0551	-0.0494	0.1264	-0.0724	0.1641	105.9738	-18.2815	94.263
2	0.0024	-0.0016	0.0022	0.0055	-0.0002	0.0008	-0.0458	0.0443	-0.0316	0.078	0.0012	-0.0184	0.0936	-0.0575	-0	0.6167	-0.2112	0.0891	0.3445	-0.0322	0.3416	96.0039	-49.6703	122.0664
3	0.0024	0.005	-0.0013	0.004	-0.0018	0.0013	-0.022	-0.0239	-0.0494	0.018	-0.035	-0.0169	0.0062	-0.0624	-0.0001	0.4614	-0.0243	-0.0108	0.2513	0.0229	0.2147	100.2588	-36.0846	135.1259
4	0.0139	-0.0023	0.0008	0.0018	-0.0004	0.0044	0.0197	-0.0556	-0.0061	0.0172	0.0219	-0.0211	-0.0145	-0.0636	0.0234	0.397	-0.0277	0.0132	0.1827	0.0266	0.036	108.318	-26.0599	134.5628
5	0.0123	0.0008	-0.0013	0.0029	-0.0006	0.0013	0.0204	0.0285	-0.0319	0.0254	0.0125	0.0081	0.0187	-0.0276	0.0078	0.2295	-0.0798	0.0566	0.176	-0.0418	0.1647	109.5949	-31.4268	117.9287
6	0.034	-0.0192	-0.0275	0.0989	-0.0258	0.043	0.0048	-0.0646	0.002	0.1456	-0.1818	0.2275	0.2465	-0.2122	-0.2211	0.1231	-0.2771	0.03	0.2191	-0.2677	0.2292	90.8604	-34.7714	111.2436
7	0.0052	0.0066	0.0005	0.0324	0.0329	0.0337	-0.0192	0.0129	-0.0239	-0.0026	0.1256	0.0481	0.0321	0.0544	0.0069	0.1218	-0.0097	0.0041	0.1011	0.0055	0.1603	52.7889	-22.4773	99.0352
8	0.0029	0.0002	-0.0035	0.0013	-0.0011	0.0018	-0.046	-0.0067	0.0023	-0.0043	-0.0161	0.0045	-0.0058	-0.0065	-0	0.2257	0.0301	-0.0392	0.1922	0.0433	0.1813	43.1389	-14.3065	96.6935
9	0.0296	-0.027	-0.0501	0.042	0.0801	0.1254	-0.0505	-0.0927	0.0629	0.0164	0.0872	0.1278	0.0024	0.0851	0.0019	0.1127	-0.0207	0.0067	0.1306	-0.0178	0.213	50.2709	-6.6272	109.8667
10	0.0228	0.0077	-0.0108	0.0503	0.0221	0.0224	0.0316	0.0366	-0.0155	-0.0767	0.008	-0.007	0.0598	0.0092	0	0.1289	0.004	-0.0131	0.1274	-0.0157	0.1352	70.0903	-7.2413	89.8248
11	0.0006	0.0013	0.0021	0.037	-0.0191	0.0233	-0.0021	0.0155	-0.035	-0.0771	0.0133	0.03	0.0075	-0.0397	0.015	0.2053	0.0157	-0.0584	0.1794	-0.0582	0.1183	62.9651	-10.9925	78.3039
12	0.001	0	0.0007	0.001	-0.0016	0.0012	-0.0243	-0.0156	-0.0107	0.0047	-0.0372	-0.015	-0.0023	-0.0031	-0	0.1542	-0.0129	-0.0214	0.1389	0.0308	0.2194	55.9311	-19.5792	106.0796
13	0.0196	0.0297	0.0202	0.0416	0.0393	0.046	-0.0381	-0.0229	0.0574	0.1057	0.0841	-0.0452	-0.075	0.0594	0.0093	0.3161	-0.0207	0.1087	0.172	-0.1044	0.1321	77.0593	15.8916	122.0083
14	0.0954	-0.0054	-0.0313	0.0468	-0.016	0.0194	0.0757	-0.0066	0.0087	0.0433	0.0364	-0.0436	0.0413	0.0453	0.0152	0.3314	0.0053	-0.0089	0.2403	-0.0434	0.0903	77.1571	5.258	132.2084
15	0.1031	0.1513	-0.0698	0.2174	-0.107	0.0549	0.0436	0.0297	-0.0065	0.0976	0.0952	0.0882	0.1038	-0.04	0.0418	0.214	-0.0261	0.0155	0.1765	-0.03	0.0919	66.8298	-0.7645	122.1402
16	0.0275	-0.0047	0.0605	0.0938	-0.0923	0.215	0.0597	0.0322	-0.033	0.1221	0.0416	0.0042	-0.084	0.2313	0.1463	0.1006	-0.0097	0.0086	0.1683	-0.0819	0.1286	83.2456	6.1482	105.422
17	0.0538	0.0064	-0.0313	0.0051	-0.0058	0.0187	0.0589	0.0167	0.0772	-0.0423	-0.0501	-0.0092	-0.0362	0.0093	0.0164	0.1747	0.0229	-0.0387	0.0635	0.013	0.168	114.9444	-1.4818	99.1361
18	0.0104	-0.0011	0.0054	0.0034	-0.0028	0.0024	-0.0512	-0.0219	0.034	0.05	-0.0673	-0.0365	0.009	0.0249	-0	0.1785	-0.0067	-0.0175	0.1381	-0.0093	0.2146	129.0362	-12.7053	102.5536
19	0.017	-0.005	-0.0054	0.0289	0.0004	0.0345	-0.0736	-0.05	-0.0571	0.0524	-0.0263	-0.0407	0.0473	-0.0389	-0.0004	0.1339	-0.0166	0.0007	0.1436	0.0027	0.1529	124.2691	-21.2888	111.7392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 141 through 285 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 1 through 28 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 29 through 61 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 62 through 113 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 114 through 140 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 141 through 285 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 2 through 44 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 45 through 61 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 62 through 140 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 141 through 234 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 235 through 263 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 264 through 286 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 46 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 47 through 75 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 76 through 140 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 141 through 285 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 2 through 28 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 29 through 61 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 62 through 140 )

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