PDB-9fol: Succinyl-CoA:(R)-benzylsuccinate CoA-transferase (BbsEF), D178-Co...

ID or keywords:

Entry

Database: PDB / ID: 9fol

Title

Succinyl-CoA:(R)-benzylsuccinate CoA-transferase (BbsEF), D178-CoA adduct + succinate (weakly occupied)

Components

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

Keywords

TRANSFERASE / CoA transferase / toluene degradation

Function / homology

Function and homology information

CoA-transferase activity
Similarity search - Function

Biological species

Aromatoleum aromaticum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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 12, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fol.cif.gz	656.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9fol.ent.gz	539.5 KB	Display	PDB format
PDBx/mmJSON format	9fol.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fo/9fol ftp://data.pdbj.org/pub/pdb/validation_reports/fo/9fol	HTTPS FTP

-
Related structure data

Related structure data	9fn0C 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

-
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

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	92.210, 100.630, 192.160
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
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 (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 (bacteria) / Gene: bbsF, c2A311 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5P688

-
Non-polymers , 6 types, 780 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#6: 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
#7: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 10000, Tris/HCl pH 8.5, glycerol

-
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: Mar 16, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 157123 / % possible obs: 94.8 % / Redundancy: 3.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.055 / Net I/σ(I): 13.86

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.8-1.9	0.629	24193	0.713	0.761	1
1.9-2	0.375	19622	0.863	0.451	1
2-2.2	0.204	28954	0.95	0.247	1
2.2-2.5	0.102	27429	0.986	0.123	1
2.5-3	0.052	24267	0.996	0.063	1
3-3.8	0.03	16629	0.998	0.037	1
3.8-4.7	0.025	7410	0.998	0.03	1
4.7-6	0.022	4420	0.999	0.027	1
6-8	0.023	2389	0.999	0.027	1
8-12	0.02	1252	0.999	0.024	1
12-50	0.02	558	0.999	0.024	1

-
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: 1.8→48.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2134	7848	5 %
R_work	0.1831	-	-
obs	0.1847	157031	94.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→48.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12578	0	246	758	13582

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_d	0.97
X-RAY DIFFRACTION	f_dihedral_angle_d	15.107	4870
X-RAY DIFFRACTION	f_chiral_restr	0.053	1881
X-RAY DIFFRACTION	f_plane_restr	0.009	2373

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 (%)
1.8-1.82	0.3118	245	0.2999	5149	X-RAY DIFFRACTION	99
1.82-1.84	0.3358	292	0.3005	5082	X-RAY DIFFRACTION	98
1.84-1.86	0.3241	281	0.2855	5085	X-RAY DIFFRACTION	98
1.86-1.89	0.2981	261	0.261	5118	X-RAY DIFFRACTION	98
1.89-1.91	0.3244	239	0.2578	5120	X-RAY DIFFRACTION	99
1.91-1.94	0.289	270	0.2497	5127	X-RAY DIFFRACTION	99
1.94-1.97	0.2664	248	0.249	5176	X-RAY DIFFRACTION	99
1.97-2	0.3036	260	0.2548	5091	X-RAY DIFFRACTION	98
2-2.03	0.2758	265	0.2362	5121	X-RAY DIFFRACTION	98
2.03-2.06	0.2571	238	0.2193	5101	X-RAY DIFFRACTION	97
2.06-2.1	0.2674	283	0.2132	5081	X-RAY DIFFRACTION	97
2.1-2.13	0.2335	271	0.2012	5061	X-RAY DIFFRACTION	97
2.13-2.18	0.2329	275	0.1931	4993	X-RAY DIFFRACTION	97
2.18-2.22	0.2436	277	0.1955	4993	X-RAY DIFFRACTION	96
2.22-2.27	0.2323	269	0.1882	4999	X-RAY DIFFRACTION	96
2.27-2.32	0.2215	269	0.1864	5010	X-RAY DIFFRACTION	96
2.32-2.38	0.2147	279	0.1863	4957	X-RAY DIFFRACTION	95
2.38-2.44	0.2178	241	0.1882	4967	X-RAY DIFFRACTION	95
2.44-2.51	0.217	272	0.1888	4915	X-RAY DIFFRACTION	94
2.51-2.6	0.2233	245	0.1864	4977	X-RAY DIFFRACTION	95
2.6-2.69	0.2164	262	0.1809	4882	X-RAY DIFFRACTION	94
2.69-2.8	0.2167	254	0.1807	4883	X-RAY DIFFRACTION	92
2.8-2.92	0.2179	271	0.173	4792	X-RAY DIFFRACTION	92
2.92-3.08	0.212	260	0.1826	4854	X-RAY DIFFRACTION	92
3.08-3.27	0.2047	274	0.1806	4810	X-RAY DIFFRACTION	91
3.27-3.52	0.2039	269	0.1639	4757	X-RAY DIFFRACTION	91
3.52-3.88	0.1876	245	0.157	4751	X-RAY DIFFRACTION	89
3.88-4.44	0.1657	235	0.1453	4676	X-RAY DIFFRACTION	88
4.44-5.59	0.1737	234	0.1489	4767	X-RAY DIFFRACTION	88
5.59-48.67	0.1938	264	0.1891	4888	X-RAY DIFFRACTION	87

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	1.2404	0.065	0.0948	1.2634	-0.3023	1.2204	0.1012	0.3265	-0.4747	-0.3837	-0.0687	-0.0533	0.3916	0.1614	-0.0344	0.4174	0.0483	0.0198	0.2658	-0.1303	0.3588	-13.2548	-28.986	14.3822
2	0.3106	0.178	0.1706	0.5334	-0.1844	0.3661	0.0294	0.0531	-0.0484	-0.0368	-0.0078	-0.082	0.1129	0.0446	-0.0234	0.2277	0.0006	0.0166	0.2229	-0.0391	0.2015	-14.8985	-10.3582	28.3038
3	0.9939	-0.0736	-0.0248	2.1246	-0.1126	0.4031	0.055	0.1478	-0.0643	-0.326	-0.0136	-0.042	0.0957	0.101	-0.0361	0.2259	0.0119	0.0087	0.2816	-0.0165	0.15	-14.5096	-0.2189	13.5342
4	2.0157	-0.3284	-0.4027	1.3948	0.8889	2.1539	0.1096	0.1452	0.2656	-0.074	-0.0961	-0.2282	-0.2736	0.2293	-0.0039	0.232	-0.0065	0.0427	0.3523	0.0296	0.3503	5.8871	-3.2249	31.971
5	1.2785	-0.5555	0.2469	1.3263	-0.3523	1.059	-0.0099	0.179	0.0067	-0.1659	-0.0419	-0.3119	0.0504	0.2917	0.0493	0.2961	0.0283	0.0612	0.33	-0.0197	0.2536	-3.4483	-4.118	16.0709
6	1.4576	-0.0692	-0.0859	1.01	-0.0751	1.1931	0.0004	0.0736	-0.054	-0.1091	0.0004	-0.0435	0.0218	0.0795	0.0073	0.256	0.0034	0.0203	0.1707	-0.0181	0.2006	-19.2018	-14.1242	32.4409
7	1.8104	0.4982	-0.3805	2.0517	-0.4873	1.7076	-0.0212	-0.3535	0.4785	0.2147	0.0928	-0.0892	-0.2476	-0.0206	-0.0691	0.2417	0.0534	-0.0365	0.2628	-0.1207	0.3101	-9.3025	27.5337	-15.5202
8	1.1535	-0.234	0.4535	1.0048	0.562	1.4823	-0.02	-0.0641	0.1682	0.0383	0.0347	-0.1465	0.0133	-0.021	-0.0117	0.1509	0.0162	0.0073	0.1664	-0.013	0.1891	-11.2907	15.4112	-31.755
9	1.3461	-0.0008	0.7809	1.4551	-0.2841	2.3582	0.1716	-0.0346	-0.1494	-0.0769	0.0227	-0.0715	0.8106	0.0516	-0.2019	0.475	0.0635	0.0024	0.3197	-0.0364	0.1788	-14.2986	0.6838	-17.5457
10	2.0937	-0.0093	0.9751	1.1499	0.5897	1.8239	0.1143	0.1046	-0.2001	-0.1168	-0.011	-0.1418	0.2048	0.0998	-0.109	0.1873	0.0351	-0.0026	0.1766	-0.0147	0.217	2.426	0.6417	-37.9655
11	1.5749	-0.6516	0.2135	2.4434	0.6	0.9895	0.0962	-0.2492	-0.2881	0.2085	0.0627	-0.2165	0.3292	0.0546	-0.1422	0.2911	0.0134	-0.0601	0.2331	0.0061	0.3139	13.6564	-5.7988	-25.3122
12	1.7522	0.0596	-0.4047	0.9913	-0.0665	0.6777	-0.0592	-0.1914	0.016	0.182	0.0926	-0.1076	0.1809	0.072	-0.0383	0.2637	0.0309	-0.013	0.2625	-0.0323	0.1871	-6.032	3.7324	-19.7589
13	1.0003	-0.236	0.3622	1.0551	0.2163	0.8686	-0.0753	-0.2887	0.0412	0.1737	-0.0021	0.1089	-0.0193	-0.2247	0.0658	0.1911	-0.0063	0.01	0.3014	-0.0321	0.2173	-30.309	14.0339	-28.548
14	1.8316	-0.4379	-0.258	1.072	0.1016	1.271	-0.0103	-0.164	0.1783	0.0782	0.0275	0.1683	-0.136	-0.2729	-0.0166	0.1857	0.0128	-0.0115	0.2433	-0.0195	0.2283	-30.0356	21.5136	-35.6717
15	1.3109	-1.3743	0.3854	1.4382	-0.4051	0.3031	0.1593	0.1553	0.1193	-0.1947	-0.0919	-0.348	0.1569	0.1841	-0.0677	0.2297	0.0455	0.034	0.2461	-0.0184	0.2769	10.2471	2.0715	-42.0042

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 141 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 142 through 239 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 240 through 408 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 109 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 110 through 228 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 229 through 409 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 2 through 107 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 108 through 239 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 240 through 409 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 5 through 79 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 80 through 124 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 125 through 228 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 229 through 263 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 264 through 349 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 350 through 409 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

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

-
Non-polymers , 6 types, 780 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

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

-Non-polymers , 6 types, 780 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

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

-
Non-polymers , 6 types, 780 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi