PDB-6mso: Crystal structure of mitochondrial fumarate hydratase from Leishm...

ID or keywords:

Entry

Database: PDB / ID: 6mso

Title

Crystal structure of mitochondrial fumarate hydratase from Leishmania major in a complex with inhibitor thiomalate

Components

fumarate hydratase

Keywords

LYASE/LYASE inhibitor / inhibitor / mitochondrial / fumarate hydratase / LYASE / LYASE-LYASE inhibitor complex

Function / homology

Function and homology information

fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.053 Å

Authors

Feliciano, P.R. / Drennan, C.L. / Nonato, M.C.

Funding support

Brazil,

United States, 5items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2014/22246-4	Brazil
Sao Paulo Research Foundation (FAPESP)	2013/14988-8	Brazil
Sao Paulo Research Foundation (FAPESP)	2008/08262-6	Brazil
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35 GM126982	United States
Howard Hughes Medical Institute (HHMI)		United States

Citation

Journal: ACS Chem. Biol. / Year: 2019
Title: Crystal Structures of Fumarate Hydratases from Leishmania major in a Complex with Inhibitor 2-Thiomalate.
Authors: Feliciano, P.R. / Drennan, C.L. / Nonato, M.C.

History

Deposition	Oct 17, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mso.cif.gz	833.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6mso.ent.gz	687.4 KB	Display	PDB format
PDBx/mmJSON format	6mso.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6mso_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	6mso_full_validation.pdf.gz	2.7 MB	Display
Data in XML	6mso_validation.xml.gz	89.7 KB	Display
Data in CIF	6mso_validation.cif.gz	123.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ms/6mso ftp://data.pdbj.org/pub/pdb/validation_reports/ms/6mso	HTTPS FTP

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Related structure data

Related structure data	6msnC 5l2rS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6uoi-d 6uqm-d 6upm-d 6msn-d 6upo-d 6uq8-d 3czp-d 5l2r-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
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (3) #127 - Jul 2010 Crystallins similarity (2)

Deposited unit

A: fumarate hydratase

B: fumarate hydratase

C: fumarate hydratase

D: fumarate hydratase

hetero molecules

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

1

A: fumarate hydratase

B: fumarate hydratase

hetero molecules

defined by author&software
Evidence: gel filtration
133 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: fumarate hydratase

D: fumarate hydratase

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.741, 138.443, 138.073
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	fumarate hydratase Mass: 64713.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_24_0320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QAU9, fumarate hydratase

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Non-polymers , 5 types, 893 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Chemical	ChemComp-JYD / (2S)-2-sulfanylbutanedioic acid / thiomalate Mass: 150.153 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₄S / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.91 Å³/Da / Density % sol: 57.69 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 2.2 M ammonium sulfate, 4 % PEG 400, 10 mM RS-thiomalate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 180831 / % possible obs: 98.6 % / Redundancy: 6.3 % / R_sym value: 0.15 / Net I/σ(I): 9.75
Reflection shell	Resolution: 2.05→2.09 Å / Mean I/σ(I) obs: 1.33 / CC_1/2: 0.706 / R_sym value: 0.605

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5L2R

5l2r

Resolution: 2.053→48.881 Å / Cross valid method: FREE R-VALUE / σ(F): 186.13 / Phase error: 20.15

	R_factor	Num. reflection	% reflection
R_free	0.2045	9156	5.06 %
R_work	0.1594	-	-
obs	0.1668	180803	98.1 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.053→48.881 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16335	0	222	867	17424

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	17039
X-RAY DIFFRACTION	f_angle_d	1.021	23051
X-RAY DIFFRACTION	f_dihedral_angle_d	8.675	14135
X-RAY DIFFRACTION	f_chiral_restr	0.057	2510
X-RAY DIFFRACTION	f_plane_restr	0.007	3000

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 (%)
2.0542-2.0896	0.2388	418	0.2039	7778	X-RAY DIFFRACTION	84
2.0896-2.1276	0.2346	446	0.1976	8439	X-RAY DIFFRACTION	92
2.1276-2.1686	0.2315	441	0.1913	8473	X-RAY DIFFRACTION	93
2.1686-2.2128	0.2307	448	0.1894	8552	X-RAY DIFFRACTION	94
2.2128-2.2609	0.2212	444	0.1845	8692	X-RAY DIFFRACTION	94
2.2609-2.3135	0.2171	452	0.1755	8606	X-RAY DIFFRACTION	94
2.3135-2.3714	0.224	449	0.1792	8468	X-RAY DIFFRACTION	93
2.3714-2.4355	0.2177	458	0.1725	8606	X-RAY DIFFRACTION	94
2.4355-2.5072	0.2136	450	0.1736	8681	X-RAY DIFFRACTION	95
2.5072-2.5881	0.2208	467	0.1711	8620	X-RAY DIFFRACTION	94
2.5881-2.6806	0.251	443	0.1698	8644	X-RAY DIFFRACTION	94
2.6806-2.7879	0.2014	454	0.1693	8692	X-RAY DIFFRACTION	94
2.7879-2.9148	0.2284	468	0.1616	8718	X-RAY DIFFRACTION	94
2.9148-3.0684	0.219	452	0.1592	8461	X-RAY DIFFRACTION	92
3.0684-3.2606	0.2135	454	0.1582	8687	X-RAY DIFFRACTION	95
3.2606-3.5123	0.2046	458	0.1575	8708	X-RAY DIFFRACTION	95
3.5123-3.8657	0.1829	472	0.1572	8735	X-RAY DIFFRACTION	95
3.8657-4.4247	0.2011	455	0.1418	8637	X-RAY DIFFRACTION	94
4.4247-5.5734	0.1666	464	0.1449	8721	X-RAY DIFFRACTION	94
5.5734-48.8953	0.2032	464	0.1756	8780	X-RAY DIFFRACTION	94

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	1.2729	0.034	-0.9751	0.626	-0.8233	3.4008	0.0258	-0.1467	0.1686	0.1484	-0.0262	0.1109	-0.2174	0.0223	-0.0017	0.1149	0.0241	0.0305	0.1259	-0.0799	0.3692	99.2022	24.5141	78.2441
2	0.7388	0.0218	-0.0729	0.1624	-0.0323	0.2146	0.0035	-0.0374	0.0361	0.0803	-0.0125	0.1146	-0.0655	-0.0414	-0.0021	-0.0353	0.0185	-0.0078	0.1227	-0.0234	0.3421	96.5593	4.2728	68.5161
3	0.3552	0.1207	0.0765	0.052	-0.0016	0.0988	-0.0204	0.0299	0.0644	0.004	-0.0069	0.1009	-0.0333	-0.1209	-0.0172	0.0014	0.02	0.0014	0.1632	0.0019	0.3793	91.2936	6.6828	61.413
4	0.7875	-0.044	-0.0026	0.2252	0.1741	0.5036	0.0506	-0.0111	-0.1554	0.0094	-0.0719	0.2175	0.0609	-0.0875	0.0091	0.0885	-0.02	-0.0107	0.1353	-0.0058	0.393	91.4149	-23.1449	66.7165
5	2.0778	1.7038	-0.3483	1.6823	-0.5015	0.2206	0.076	-0.2227	0.1488	0.2294	-0.0914	0.0848	-0.0972	0.0246	0.0163	0.1225	-0.0054	-0.0583	0.1662	-0.0571	0.2741	119.6331	19.5232	82.5732
6	0.6196	0.0995	-0.1321	0.086	0.0144	0.2658	-0.0081	0.0596	0.0452	0.0129	-0.0099	-0.0402	-0.0563	0.0566	-0.0013	-0.0263	-0.0112	-0.0112	0.1308	-0.0045	0.3453	126.6029	17.5306	59.2817
7	0.5989	-0.0732	-0.0157	0.1825	-0.0289	0.1559	0.0185	-0.0049	-0.0387	0.0264	-0.0271	0.0108	0.0024	0.0179	0.0041	0.0188	0.0105	-0.0056	0.1332	-0.0128	0.3072	116.1977	4.765	62.5332
8	1.7536	0.0731	-0.9276	0.1303	0.051	0.9545	-0.0199	-0.0936	-0.0514	0.0134	0.0034	-0.0626	0.0246	0.0936	0.0154	0.0359	0.0121	-0.0278	0.1184	0.0018	0.3009	123.6928	-1.9014	66.0341
9	0.8575	0.0653	0.0321	0.1796	0.0293	0.3674	-0.0344	0.0566	0.0785	0.0219	0.06	-0.0198	-0.051	0.0887	0.0456	0.0195	0.0036	-0.0312	0.1163	-0.009	0.2861	126.1746	10.9036	68.1285
10	1.9365	0.0036	0.4103	0.3619	0.2013	0.5232	0.0342	0.3818	-0.0775	-0.1537	0.0365	-0.0772	-0.0172	0.1829	-0.0576	0.1246	-0.0031	0.0359	0.3056	-0.0136	0.2285	127.2335	8.779	35.1199
11	2.2093	1.5441	0.4826	4.0269	0.472	0.885	-0.0983	-0.1115	0.0384	-0.0798	0.0697	0.4114	0.1379	-0.3738	0.0378	0.2169	-0.0739	0.0119	0.5127	0.0987	0.2124	78.7197	5.2949	148.8654
12	0.0432	0.1681	-0.2449	1.4566	-0.6592	1.525	0.0443	-0.0545	-0.0984	0.0398	-0.0804	-0.0028	0.0864	-0.0327	0.0312	0.1242	-0.0391	-0.0069	0.3478	0.0453	0.3033	75.8033	3.0865	130.9796
13	0.3639	0.347	0.364	0.5124	0.2356	0.4441	0.0165	-0.0772	0.0534	0.0368	-0.0626	0.0032	-0.0251	-0.1497	0.0437	0.1383	0.0335	0.0192	0.3429	-0.0072	0.3145	83.2234	19.1167	134.3841
14	1.1046	-0.1595	0.7292	0.3122	0.0267	0.5827	-0.0481	-0.1192	0.0728	0.0868	0.0191	0.2986	-0.0573	-0.1855	0.027	0.1459	0.0216	0.0523	0.362	-0.025	0.3298	74.9462	19.3288	133.9857
15	2.1194	-0.2575	-0.9948	0.7127	0.191	0.89	0.0983	0.2239	0.0489	-0.0995	0.0495	0.2173	-0.0365	-0.3496	-0.1316	0.1561	0.0179	-0.0187	0.3511	0.0174	0.3159	74.7842	12.4753	103.4098
16	3.7394	-0.4311	-1.7126	2.9835	-0.9057	1.4619	-0.0159	0.0742	0.0247	0.0163	0.1893	0.2407	-0.0122	-0.2378	-0.1749	0.1323	0.0121	-0.0744	0.3933	-0.0202	0.2143	73.6091	13.6481	105.3018
17	1.7821	0.8255	2.3688	0.4398	1.124	3.2077	0.1303	-0.1735	-0.2389	0.0374	0.0217	-0.0682	0.3002	-0.0786	-0.1394	0.1665	0.0274	-0.0313	0.3309	0.0372	0.3158	104.21	2.6652	148.7679
18	0.1043	0.3069	-0.1337	1.0212	-0.3188	1.289	0.0092	-0.0136	0.1016	0.0561	0.064	-0.0842	-0.0238	0.1341	-0.0746	0.1021	-0.0071	-0.0142	0.3091	0.015	0.3207	106.5089	20.4028	143.9323
19	3.7127	2.294	1.4653	1.7289	0.5703	1.0228	-0.0133	0.1469	-0.066	-0.0591	0.0036	-0.124	0.0415	0.1737	0.0183	0.145	0.0556	0.0516	0.2721	-0.0197	0.2556	104.207	15.5153	123.0697
20	1.288	0.1984	0.2814	1.0547	0.1227	0.4997	-0.0851	-0.009	0.3842	-0.0219	0.0117	-0.1172	-0.1861	0.225	0.0661	0.1896	-0.0227	0.0223	0.3611	0.0211	0.4128	109.8693	34.7746	137.9818
21	3.7784	-0.8053	0.3226	1.7459	-1.2683	2.0964	0.0649	0.3764	0.5504	0.0831	-0.1701	-0.2076	-0.3284	0.2666	0.0942	0.1976	-0.0441	0.006	0.2709	0.0197	0.4837	107.8547	44.2612	134.4624

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 279 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 280 through 355 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 356 through 549 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 52 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 53 through 165 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 166 through 228 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 229 through 312 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 313 through 355 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 356 through 549 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 12 through 39 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 40 through 165 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 166 through 279 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 280 through 351 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 352 through 478 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 479 through 548 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 12 through 69 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 70 through 201 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 202 through 312 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 313 through 451 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 452 through 548 )

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Movie

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Structure viewers

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Viewer log

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Open data

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Download

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Validation report

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Links

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Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 893 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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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