PDB-9br6: Crystal structure of human succinyl-CoA:glutarate-CoA transferase...

ID or keywords:

Entry

Database: PDB / ID: 9br6

Title

Crystal structure of human succinyl-CoA:glutarate-CoA transferase (SUGCT)

Components

Succinate--hydroxymethylglutarate CoA-transferase

Keywords

TRANSFERASE / SUGCT / succinyl-CoA / glutarate

Function / homology

succinate-hydroxymethylglutarate CoA-transferase / succinate-hydroxymethylglutarate CoA-transferase activity / : / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / mitochondrion / Succinate--hydroxymethylglutarate CoA-transferase

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Khamrui, S. / Lazarus, M.B.

Funding support

United States, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2024
Title: Characterization, Structure, and Inhibition of the Human Succinyl-CoA:glutarate-CoA Transferase, a Putative Genetic Modifier of Glutaric Aciduria Type 1.
Authors: Wu, R. / Khamrui, S. / Dodatko, T. / Leandro, J. / Sabovic, A. / Violante, S. / Cross, J.R. / Marsan, E. / Kumar, K. / DeVita, R.J. / Lazarus, M.B. / Houten, S.M.

History

Deposition	May 10, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9br6.cif.gz	322.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9br6.ent.gz	264.3 KB	Display	PDB format
PDBx/mmJSON format	9br6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9br6_validation.pdf.gz	436.7 KB	Display	wwPDB validaton report
Full document	9br6_full_validation.pdf.gz	440.7 KB	Display
Data in XML	9br6_validation.xml.gz	27.3 KB	Display
Data in CIF	9br6_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/9br6 ftp://data.pdbj.org/pub/pdb/validation_reports/br/9br6	HTTPS FTP

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Related structure data

Related structure data	9br7C C: citing same article (ref.)
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

Deposited unit

A: Succinate--hydroxymethylglutarate CoA-transferase

B: Succinate--hydroxymethylglutarate CoA-transferase

89.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	91.083, 115.126, 79.220
Angle α, β, γ (deg.)	90.00, 100.79, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Succinate--hydroxymethylglutarate CoA-transferase / Dermal papilla-derived protein 13 / SuccinylCoA:glutarate-CoA transferase Mass: 44873.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUGCT, C7orf10, DERP13 / Production host: Escherichia coli (E. coli) References: UniProt: Q9HAC7, succinate-hydroxymethylglutarate CoA-transferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Succinate--hydroxymethylglutarate CoA-transferase / Dermal papilla-derived protein 13 / SuccinylCoA:glutarate-CoA transferase

Mass: 44873.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SUGCT, C7orf10, DERP13 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q9HAC7, succinate-hydroxymethylglutarate CoA-transferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.27 Å³/Da / Density % sol: 45.89 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M Tris, pH 8.5, 25% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2023
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.920105 Å / Relative weight: 1
Reflection	Resolution: 2.4→48.84 Å / Num. obs: 31313 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.11 / R_pim(I) all: 0.068 / R_rim(I) all: 0.13 / Χ²: 0.99 / Net I/σ(I): 7 / Num. measured all: 110121
Reflection shell	Resolution: 2.4→2.49 Å / % possible obs: 99.8 % / Redundancy: 3.2 % / R_merge(I) obs: 1.593 / Num. measured all: 10391 / Num. unique obs: 3265 / CC_1/2: 0.406 / R_pim(I) all: 1.069 / R_rim(I) all: 1.925 / Χ²: 1.02 / Net I/σ(I) obs: 0.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→44.74 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.239	1521	4.87 %
R_work	0.2211	-	-
obs	0.222	31264	99.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.4→44.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6214	0	0	5	6219

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003
X-RAY DIFFRACTION	f_angle_d	0.532
X-RAY DIFFRACTION	f_dihedral_angle_d	10.807	2355
X-RAY DIFFRACTION	f_chiral_restr	0.043	965
X-RAY DIFFRACTION	f_plane_restr	0.005	1114

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 (%)
2.4-2.48	0.431	149	0.3927	2684	X-RAY DIFFRACTION	100
2.48-2.57	0.3801	148	0.3702	2668	X-RAY DIFFRACTION	100
2.57-2.67	0.396	142	0.3302	2674	X-RAY DIFFRACTION	100
2.67-2.79	0.3627	137	0.3188	2705	X-RAY DIFFRACTION	100
2.79-2.94	0.3038	119	0.2999	2758	X-RAY DIFFRACTION	100
2.94-3.12	0.3149	133	0.2878	2658	X-RAY DIFFRACTION	100
3.12-3.36	0.2608	133	0.248	2725	X-RAY DIFFRACTION	100
3.36-3.7	0.2557	124	0.2296	2715	X-RAY DIFFRACTION	100
3.7-4.24	0.2027	141	0.1899	2724	X-RAY DIFFRACTION	100
4.24-5.33	0.1932	167	0.1684	2679	X-RAY DIFFRACTION	99
5.34-44.74	0.1747	128	0.1648	2753	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	3.9373	4.3392	0.2296	4.7688	0.2612	0.1103	0.6566	-1.7924	-1.2756	-1.2197	-0.7819	3.2005	0.9537	0.61	0.6434	1.041	-0.107	-0.1829	0.9748	-0.0733	1.9116	3.064	-19.405	32.135
2	6.2164	2.1615	0.335	2.0441	2.5258	8.9869	0.122	-0.4547	0.3601	-0.4744	0.2806	0.6953	-0.0522	-0.138	-0.2084	0.4493	-0.0226	0.0027	0.6119	0.1308	0.7988	12.924	-3.208	37.256
3	2.9853	0.6001	1.6786	3.7337	1.6118	3.7945	0.0712	-0.6426	0.4548	-0.1243	-0.1369	-0.1476	-0.3858	-0.1256	0.0548	0.3805	-0.0308	-0.0019	0.5488	0.0523	0.6349	8.486	5.653	29.561
4	2.5859	-0.4217	3.1577	4.8375	0.3712	6.2983	-0.361	-0.0468	0.5275	0.4354	0.1665	-0.0464	-0.2305	0.7877	0.1679	0.5172	-0.0405	-0.0039	0.8447	0.09	0.6334	13.817	7.813	47.871
5	2.4268	2.2883	-1.7123	3.2717	-0.6604	3.8601	0.1301	-0.8232	0.0829	-0.0551	-0.1694	0.0882	-0.1633	0.1425	-0.0052	0.401	0.003	-0.1113	0.7703	0.0569	0.8363	25.391	4.931	37.868
6	1.7677	0.0263	-0.0902	2.1571	-1.2043	2.2532	0.0578	-0.2518	-0.2401	-0.2465	0.0784	-0.2833	0.146	0.0433	-0.2054	0.4857	-0.039	-0.0175	0.509	-0.0179	0.791	24.24	2.589	17.409
7	4.9419	4.0048	4.3466	3.2999	3.4082	4.2021	0.0216	-1.2114	1.4203	-0.2849	-0.6397	-1.6171	0.3219	-0.4491	0.5134	0.6131	0.1793	0.0239	1.1185	0.3291	1.2396	24.738	-14.928	42.555
8	0.715	-0.0673	1.299	0.4064	-0.4721	3.6838	0.1476	0.0752	-0.0129	-0.0465	-0.0123	-0.4256	-0.029	-0.1437	-0.1395	0.4278	-0.0374	0.0303	0.6043	0.0811	0.9367	32.969	-0.429	15.192
9	6.6507	7.663	1.8424	8.9614	1.6297	2.3653	-0.1833	-0.0517	-0.7844	1.553	-0.7785	-1.2521	0.8074	0.429	0.6393	0.4113	0.0011	0.0464	0.5252	0.0994	1.145	28.182	-5.661	-3.636
10	6.4412	-0.2673	-1.4329	6.4711	-0.1462	5.8172	0.0043	0.6754	-0.6213	-0.5373	-0.0892	-0.6649	0.2751	0.4073	0.0758	0.3186	0.0158	0.0293	0.3596	0.0183	0.5675	23.145	-6.386	-12.325
11	2.8045	-0.2326	0.6315	2.2489	1.0908	4.5612	-0.0388	0.26	-0.0056	0.1456	0.0973	-0.0062	-0.0598	-0.1079	-0.0767	0.3648	-0.0028	0.0282	0.5452	0.0596	0.6538	10.38	-5.029	-7.58
12	9.1074	-0.3928	-4.1477	0.562	1.0092	3.2069	0.0917	2.3781	-0.3587	-0.3093	-0.5599	0.7079	0.5772	-0.4799	0.0845	0.6268	0.0371	-0.0034	0.5917	0.0491	0.6168	2.873	-1.403	6.399
13	1.1129	0.3082	0.3824	0.9841	1.7926	2.6222	-0.012	-0.0301	-0.5788	-0.2189	-0.1024	0.3658	-0.022	-0.2101	0.0627	0.4337	-0.0125	0.0308	0.5543	0.1431	0.6985	1.974	-6.788	21.111
14	3.0344	-1.6958	1.6932	1.4644	1.4345	9.221	-0.3023	-0.7035	-0.1353	0.0883	-0.0674	-0.1488	0.6163	-1.1733	0.4803	0.38	-0.058	0.0218	0.8271	0.0877	0.631	2.096	1.581	41.525
15	8.5505	1.1868	0.6206	9.1679	1.3942	4.9656	-0.7346	-2.7929	1.1018	1.5676	1.3067	0.33	-0.1951	0.5264	-0.2201	0.5292	0.3147	-0.1632	1.2794	-0.2382	0.9168	3.462	10.949	53.538
16	2.774	-2.9188	3.1632	3.2614	-3.368	3.8093	0.1359	-1.6749	0.6408	0.3648	0.3424	2.4029	-0.5795	-2.2813	-0.4301	0.7356	0.0924	0.0013	1.136	0.0117	0.757	-2.36	10.165	41.013
17	5.0179	2.9195	5.6824	2.3253	2.9731	6.618	1.7845	1.038	1.2332	1.3166	0.0745	-0.1526	-0.555	-0.146	-1.8034	1.8742	0.3485	0.5985	1.5448	0.2453	2.2111	35.192	-16.998	43.378
18	6.3021	5.7491	2.1979	8.7931	8.0553	1.9957	-0.5904	-1.4612	-0.7347	1.8974	-0.5849	-2.6044	1.689	0.8039	1.6665	0.6028	0.0712	-0.1135	0.8708	0.1698	1.2813	30.802	-17.539	34.343
19	3.0225	1.0148	-1.3389	1.9368	0.125	1.7338	-0.0262	-0.1252	-0.4551	-0.1563	0.1606	-0.3284	0.1177	0.3703	-0.0787	0.4643	0.0502	-0.0364	0.5764	0.0775	1.089	31.921	-19.143	13.575
20	2.6862	-1.9263	0.7609	2.4947	-0.2339	1.7366	-0.0741	0.0034	-0.721	0.0611	-0.0996	-0.5494	0.3603	-0.1305	0.1836	0.4103	-0.0562	-0.0022	0.4547	0.103	1.0215	16.883	-22.63	13.16
21	1.3254	-0.0822	-0.2296	3.6848	-3.3155	3.6351	0.1759	-0.251	-0.2808	0.4328	-0.2872	-0.3973	-0.4364	0.2665	0.2086	0.506	-0.0495	-0.0395	0.5361	0.0244	0.731	19.774	-3.501	14.306
22	1.9048	-0.4845	-0.1988	3.0897	-1.486	0.8474	0.27	0.012	-0.2534	-0.0196	-0.3052	0.0594	0.1351	0.1202	0.0651	0.4175	-0.013	-0.0356	0.4659	0.0803	0.6711	10.376	-4.099	17.625
23	6.7301	0.9725	-2.7577	2.034	1.3792	2.914	-0.5107	0.3414	0.4212	0.6313	0.6347	0.4897	0.5335	-0.9584	-0.4883	0.6074	-0.0179	0.0017	0.6672	0.0085	1.325	15.503	18.149	15.69
24	5.4988	-1.3743	-0.6337	7.2194	1.8506	7.1078	-0.1643	-0.3038	0.6796	0.3424	0.1564	0.2258	-0.0435	0.291	0.0239	0.5455	-0.0793	0.0516	0.5289	0.0704	0.8784	25.765	25.871	17.744
25	2.2505	-0.4252	1.5011	9.7982	-1.3087	2.0521	-0.5553	-0.9399	1.4111	1.1622	0.1049	0.1391	0.5998	-0.8965	0.7893	0.978	0.0495	0.0607	0.7239	-0.1183	1.4867	13.175	32.196	18.507
26	2.5035	-1.5114	1.1836	7.6763	1.3953	3.2217	0.0896	0.3274	0.1893	-0.2749	-0.1376	-0.357	-0.3975	0.1934	-0.1077	0.7105	-0.0919	0.0709	0.5307	0.0979	0.8489	26.831	26.804	13.812
27	2.1062	-1.0999	0.4376	2.9655	-1.5547	2.1632	-0.0777	-0.1358	0.2534	0.0339	-0.2251	-1.142	-0.4867	0.4375	0.0963	0.5752	-0.1059	-0.035	0.4639	0.0621	0.9903	36.481	8.95	20.38
28	6.0138	-4.8926	-3.858	6.6553	3.8878	3.8532	0.0286	-0.9171	-0.5699	-0.3506	0.532	-0.1557	-0.22	0.8999	-0.4639	0.5061	-0.0333	-0.0127	0.7577	0.0798	1.208	42.612	-10.571	19.076
29	1.495	0.8862	0.0187	6.6586	1.0178	6.5799	0.4157	-0.3556	-0.4358	-0.4098	-0.1236	-1.1263	0.1557	0.7138	-0.3659	0.5761	-0.0255	-0.2393	0.8934	0.0306	1.1701	34.921	-8.351	33.439
30	0.1474	0.7903	-0.2855	5.6148	0.455	2.8961	0.0081	-0.2345	-1.3611	0.1605	0.3643	0.23	0.4407	0.5118	-0.4765	0.4824	0.0791	-0.1242	0.7324	0.0726	1.3808	38.802	-26.809	17.965
31	4.5096	2.6836	-1.634	3.3584	1.9727	6.003	0.0399	-1.2855	-1.8393	0.7355	-0.8244	-2.225	1.8976	0.4285	0.7212	0.6385	0.3004	0.1355	0.4998	-0.0264	2.1428	35.8	-39.884	14.881
32	9.9194	3.8882	4.0921	3.8494	-0.4999	7.2476	-1.1732	-0.1286	-1.3238	0.8267	0.6373	-2.3773	0.197	2.2859	0.8126	0.7361	0.103	0.1087	1.003	0.0658	1.6673	44.557	-28.925	12.606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 35:39 )	A	35 - 39
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 40:51 )	A	40 - 51
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 52:104 )	A	52 - 104
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 105:125 )	A	105 - 125
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 126:177 )	A	126 - 177
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 178:221 )	A	178 - 221
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 222:228 )	A	222 - 228
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 229:264 )	A	229 - 264
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 265:270 )	A	265 - 270
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 271:327 )	A	271 - 327
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 328:355 )	A	328 - 355
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 356:361 )	A	356 - 361
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 362:396 )	A	362 - 396
14	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 397:417 )	A	397 - 417
15	X-RAY DIFFRACTION	15	( CHAIN A AND RESID 418:432 )	A	418 - 432
16	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 433:438 )	A	433 - 438
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 34:37 )	B	34 - 37
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 38:42 )	B	38 - 42
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 43:112 )	B	43 - 112
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 113:187 )	B	113 - 187
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 188:221 )	B	188 - 221
22	X-RAY DIFFRACTION	22	( CHAIN B AND RESID 222:263 )	B	222 - 263
23	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 264:269 )	B	264 - 269
24	X-RAY DIFFRACTION	24	( CHAIN B AND RESID 270:304 )	B	270 - 304
25	X-RAY DIFFRACTION	25	( CHAIN B AND RESID 305:313 )	B	305 - 313
26	X-RAY DIFFRACTION	26	( CHAIN B AND RESID 314:343 )	B	314 - 343
27	X-RAY DIFFRACTION	27	( CHAIN B AND RESID 344:370 )	B	344 - 370
28	X-RAY DIFFRACTION	28	( CHAIN B AND RESID 371:388 )	B	371 - 388
29	X-RAY DIFFRACTION	29	( CHAIN B AND RESID 389:397 )	B	389 - 397
30	X-RAY DIFFRACTION	30	( CHAIN B AND RESID 398:413 )	B	398 - 413
31	X-RAY DIFFRACTION	31	( CHAIN B AND RESID 414:433 )	B	414 - 433
32	X-RAY DIFFRACTION	32	( CHAIN B AND RESID 434:438 )	B	434 - 438

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