PDB-9fn0: Succinyl-CoA:(R)-benzylsuccinate CoA-transferase (BbsEF)

ID or keywords:

Entry

Database: PDB / ID: 9fn0

Title

Succinyl-CoA:(R)-benzylsuccinate CoA-transferase (BbsEF)

Components

(Subunit of Benzylsuccinate CoA- ...) x 2

Keywords

TRANSFERASE / CoA transferase / toluene degradation

Function / homology

CoA-transferase activity / : / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / COENZYME A / Subunit of Benzylsuccinate CoA-transferase / Subunit of Benzylsuccinate CoA-transferase

Function and homology information

Biological species

Aromatoleum aromaticum EbN1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Ermler, U. / Heider, J. / Demmer, U.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure of the succinyl-CoA:(R)-benzylsuccinate CoA-transferase
Authors: Schuehle, K. / Demmer, U. / Heider, J. / Ermler, U.

History

Deposition	Jun 7, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fn0.cif.gz	913.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9fn0.ent.gz	770 KB	Display	PDB format
PDBx/mmJSON format	9fn0.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/fn/9fn0 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/9fn0	HTTPS FTP

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Related structure data

Related structure data	9folC 9funC 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
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Subunit of Benzylsuccinate CoA-transferase

B: Subunit of Benzylsuccinate CoA-transferase

C: Subunit of Benzylsuccinate CoA-transferase

D: Subunit of Benzylsuccinate CoA-transferase

hetero molecules

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

1

A: Subunit of Benzylsuccinate CoA-transferase

B: Subunit of Benzylsuccinate CoA-transferase

hetero molecules

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

2

C: Subunit of Benzylsuccinate CoA-transferase

D: Subunit of Benzylsuccinate CoA-transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.400, 101.300, 192.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Subunit of Benzylsuccinate CoA- ... , 2 types, 4 molecules ACBD

#1: Protein	Subunit of Benzylsuccinate CoA-transferase Mass: 45443.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aromatoleum aromaticum EbN1 (bacteria) / Gene: bbsE, c2A312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5P687
#2: Protein	Subunit of Benzylsuccinate CoA-transferase Mass: 44795.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aromatoleum aromaticum EbN1 (bacteria) / Gene: bbsF, c2A311 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5P688

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Non-polymers , 4 types, 989 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 981 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.74 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEE 797, MOPS pH 6.5, CaCl2, glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 274912 / % possible obs: 95.5 % / Redundancy: 9.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / R_rim(I) all: 0.062 / Net I/σ(I): 20.54

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.5-1.6	1.517	38124	0.572	1.63	1
1.6-1.8	0.674	69429	0.921	0.711	1
1.8-2.2	0.187	74951	0.993	0.198	1
2.2-2.8	0.064	47091	0.999	0.068	1
2.8-3.6	0.037	23683	0.999	0.039	1
3.6-4.7	0.03	11717	0.999	0.032	1
4.7-5.9	0.028	4804	0.999	0.029	1
5.9-8	0.028	2991	0.999	0.029	1
8-12	0.026	1456	0.999	0.027	1
12-50	0.026	666	0.998	0.028	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→48.98 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1971	13816	5.03 %
R_work	0.1753	-	-
obs	0.1764	274789	95.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→48.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12608	0	94	981	13683

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01
X-RAY DIFFRACTION	f_angle_d	1.087
X-RAY DIFFRACTION	f_dihedral_angle_d	14.45	4743
X-RAY DIFFRACTION	f_chiral_restr	0.059	1858
X-RAY DIFFRACTION	f_plane_restr	0.012	2343

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 (%)
1.5-1.52	0.452	293	0.4567	5688	X-RAY DIFFRACTION	63
1.52-1.54	0.4216	341	0.4176	6439	X-RAY DIFFRACTION	71
1.54-1.56	0.43	355	0.3815	6941	X-RAY DIFFRACTION	77
1.56-1.57	0.3644	395	0.3692	7430	X-RAY DIFFRACTION	83
1.57-1.6	0.3442	398	0.3248	8044	X-RAY DIFFRACTION	89
1.6-1.62	0.3189	424	0.3027	8599	X-RAY DIFFRACTION	95
1.62-1.64	0.3028	504	0.2576	8862	X-RAY DIFFRACTION	99
1.64-1.66	0.2675	458	0.2357	8956	X-RAY DIFFRACTION	99
1.67-1.69	0.2573	516	0.2199	8959	X-RAY DIFFRACTION	99
1.69-1.72	0.2369	468	0.2142	8970	X-RAY DIFFRACTION	99
1.72-1.75	0.2459	469	0.2106	8944	X-RAY DIFFRACTION	99
1.75-1.78	0.2402	518	0.212	8999	X-RAY DIFFRACTION	100
1.78-1.81	0.2263	468	0.2137	8974	X-RAY DIFFRACTION	100
1.81-1.85	0.2279	486	0.2163	9014	X-RAY DIFFRACTION	100
1.85-1.89	0.2356	451	0.2116	9048	X-RAY DIFFRACTION	100
1.89-1.94	0.2113	534	0.1832	8944	X-RAY DIFFRACTION	100
1.94-1.98	0.2111	460	0.1725	9087	X-RAY DIFFRACTION	100
1.98-2.04	0.1954	493	0.1741	9009	X-RAY DIFFRACTION	100
2.04-2.1	0.1938	501	0.1691	9054	X-RAY DIFFRACTION	100
2.1-2.17	0.1857	499	0.1651	9046	X-RAY DIFFRACTION	100
2.17-2.24	0.1936	458	0.1642	9081	X-RAY DIFFRACTION	100
2.24-2.33	0.176	472	0.1631	9078	X-RAY DIFFRACTION	100
2.33-2.44	0.1996	471	0.1665	9136	X-RAY DIFFRACTION	100
2.44-2.57	0.1924	449	0.157	9147	X-RAY DIFFRACTION	100
2.57-2.73	0.1769	489	0.1577	9118	X-RAY DIFFRACTION	100
2.73-2.94	0.1872	499	0.1646	9121	X-RAY DIFFRACTION	100
2.94-3.23	0.1842	482	0.1717	9178	X-RAY DIFFRACTION	100
3.23-3.7	0.1795	486	0.1613	9235	X-RAY DIFFRACTION	100
3.7-4.66	0.153	471	0.1409	9282	X-RAY DIFFRACTION	100
4.66-48.98	0.1947	508	0.1663	9590	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	1.1454	-0.1111	0.2614	1.6997	-0.1335	0.9501	-0.0304	0.4196	-0.3757	-0.3814	0.019	-0.0565	0.2192	0.0591	-0.0034	0.4743	0.0252	0.06	0.2867	-0.1297	0.2833	-14.8806	-24.2809	8.3424
2	0.9976	0.1292	0.1257	0.3812	-0.1738	0.5839	0.0306	0.0912	-0.3217	-0.165	-0.0446	-0.1268	0.2502	0.0658	-0.0073	0.2663	0.0209	0.0495	0.1524	-0.0362	0.2355	-13.4758	-20.1546	25.585
3	1.0104	-0.0948	-0.1727	1.5708	0.1228	1.0137	0.0499	0.1048	0.1482	-0.233	0.0033	-0.0984	0.072	0.0257	-0.0434	0.1703	-0.0048	0.037	0.1855	0.0041	0.1427	-15.19	10.1279	17.3028
4	1.0087	0.1004	0.2241	1.8339	0.0775	0.7195	0.0134	0.4434	-0.8499	-0.4665	0.0039	0.1013	0.4714	0.0251	0.0454	0.7572	-0.0076	0.1646	0.4445	-0.4486	0.5504	-12.6685	-35.1099	1.0965
5	2.4014	-0.3143	-1.0152	0.8586	0.9423	2.1124	0.1512	-0.0079	0.3084	-0.1484	-0.0262	-0.245	-0.2756	0.3498	-0.1214	0.2694	-0.004	0.0876	0.3392	0.0355	0.3789	7.6119	-3.1836	30.1711
6	0.6101	0.1521	-0.1248	0.643	-0.277	0.5332	0.003	0.1143	-0.0539	-0.2109	0.0022	-0.0645	0.1063	0.0529	-0.0144	0.2176	0.0119	0.0248	0.1483	-0.0399	0.1419	-20.2575	-11.9187	24.7152
7	2.7621	-0.4509	-0.3347	0.2457	-0.5022	1.9397	0.1199	-0.3408	0.377	0.1908	-0.0718	-0.3951	-0.1614	0.7009	-0.0324	0.2522	-0.0192	0.0465	0.5171	-0.0274	0.4953	14.8465	-6.369	37.8418
8	0.8096	0.2175	-0.0689	1.2154	-0.2274	1.147	-0.0621	-0.3916	0.5316	0.162	0.0581	0.023	-0.1584	-0.1282	-0.0103	0.1992	0.0338	-0.0267	0.2843	-0.1669	0.3506	-9.3806	27.9824	-15.7473
9	0.811	-0.3152	0.4385	0.4224	0.2425	0.9107	-0.0294	-0.074	0.1962	0.0246	-0.0006	-0.0613	0.0056	-0.0737	0.0193	0.1267	-0.0011	0.0091	0.1612	-0.0325	0.1939	-11.0264	16.3008	-32.1616
10	0.486	0.0627	0.6762	0.4891	0.348	1.1051	0.5398	-0.0467	-0.4608	-0.0276	-0.0454	0.108	1.7373	0.1582	0.1894	1.2762	-0.049	-0.1927	0.3454	-0.0708	0.2408	-20.0725	-15.5124	-26.0764
11	1.0152	0.1445	0.0041	1.0758	-0.2015	1.4	-0.0847	-0.5055	0.4133	0.3208	0.1058	-0.12	-0.1538	-0.0064	0.0268	0.2644	0.0256	-0.028	0.4026	-0.1998	0.3216	-7.3436	23.0605	-6.3056
12	1.8086	-0.0458	1.0873	0.6639	0.572	1.587	0.111	0.014	-0.0839	-0.0906	-0.0349	-0.0087	0.1575	-0.0081	-0.0688	0.1682	0.0073	0.0004	0.1515	-0.0095	0.1856	2.318	0.9718	-37.9907
13	1.5648	-0.3408	0.07	2.2255	0.6572	1.1211	0.0745	-0.2121	-0.0833	0.2211	-0.0156	-0.211	0.3066	0.0623	-0.0685	0.2447	0.014	-0.0357	0.195	-0.0096	0.2131	13.5505	-5.8227	-25.2396
14	1.5173	0.0703	0.0036	0.7403	0.0388	0.5516	0.0181	-0.1827	0.0717	0.1525	0.0204	-0.0349	0.1694	-0.0229	-0.0424	0.2188	0.0017	-0.0048	0.2392	-0.0322	0.1316	-6.2022	3.934	-19.6714
15	1.493	-0.6518	1.0595	1.3013	-0.3518	0.8977	-0.0428	-0.4244	0.1002	0.2288	-0.0065	0.1449	0.025	-0.3183	-0.079	0.1601	-0.016	0.0454	0.3644	-0.0646	0.1989	-30.344	13.4969	-22.5362
16	1.2149	-0.2538	0.1277	0.7215	-0.0813	0.5939	-0.0115	-0.1523	0.1904	0.0235	0.0076	0.0975	-0.0336	-0.1867	0.0138	0.1246	0.0029	-0.0078	0.187	-0.04	0.1839	-26.6437	19.4034	-37.1071
17	1.4829	-0.9717	0.2549	1.2643	-0.2772	0.722	0.138	0.1224	0.1374	-0.1938	-0.0961	-0.3108	0.1586	0.1616	-0.0182	0.1949	0.0278	0.0345	0.2162	-0.0059	0.248	14.8133	-0.3441	-40.8539

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 239 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 240 through 367 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 368 through 409 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 124 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 125 through 365 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 366 through 409 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3 through 110 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 111 through 232 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 233 through 333 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 334 through 409 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 4 through 79 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 80 through 124 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 125 through 228 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 229 through 249 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 250 through 365 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 366 through 409 )

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Subunit of Benzylsuccinate CoA- ... , 2 types, 4 molecules ACBD

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