PDB-9g87: 3-methylbenzoyl-CoA reductase from Thauera chlorobenzoica (subuni...

ID or keywords:

Entry

Database: PDB / ID: 9g87

Title

3-methylbenzoyl-CoA reductase from Thauera chlorobenzoica (subunits MbdON )

Components

(3-methylbenzoyl-CoA reductase ...) x 2

Keywords

OXIDOREDUCTASE / anaerobic aromate degradation / Fe/S clusters / ATP

Function / homology

FldB/FldC dehydratase alpha/beta subunit / 2-hydroxyglutaryl-CoA dehydratase, D-component / iron-sulfur cluster binding / metal ion binding / benzoyl coenzyme A / IRON/SULFUR CLUSTER / 3-methylbenzoyl-CoA reductase beta subunit MbdO / 3-methylbenzoyl-CoA reductase gamma subunit MbdN

Function and homology information

Biological species

Thauera chlorobenzoica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Ermler, U. / Boll, M. / Demmer, U. / Fuchs, J.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure and mechanism of 3-methylbenzoyl-CoA reductase from Thauera chlorobenzoica
Authors: Fuchs, J. / Demmer, U. / Ermler, U. / Boll, M.

History

Deposition	Jul 23, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9g87.cif.gz	351.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9g87.ent.gz	284.7 KB	Display	PDB format
PDBx/mmJSON format	9g87.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/g8/9g87 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/9g87	HTTPS FTP

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Related structure data

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: 3-methylbenzoyl-CoA reductase beta subunit MbdO

B: 3-methylbenzoyl-CoA reductase gamma subunit MbdN

hetero molecules

96.2 kDa, 2 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)	149.630, 149.630, 97.730
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

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3-methylbenzoyl-CoA reductase ... , 2 types, 2 molecules AB

#1: Protein	3-methylbenzoyl-CoA reductase beta subunit MbdO Mass: 49839.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera chlorobenzoica (bacteria) / Gene: Tchl_3426 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1H5YRX6
#2: Protein	3-methylbenzoyl-CoA reductase gamma subunit MbdN Mass: 44111.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera chlorobenzoica (bacteria) / Gene: Tchl_3425 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1H5YT37

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Non-polymers , 5 types, 405 molecules

#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-BYC / benzoyl coenzyme A Mass: 871.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₈H₄₀N₇O₁₇P₃S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 394 / 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: 3.36 Å³/Da / Density % sol: 63.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEP426, HEPES pH 7.5, 5 mM benzoyl-CoA

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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: Sep 8, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 97582 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC_1/2: 1 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.06 / Net I/σ(I): 19.94

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.9-2	1.033	13637	0.695	1.117	1
2-2.2	0.487	20798	0.92	0.522	1
2.2-2.5	0.211	20002	0.984	0.226	1
2.5-3	0.088	18085	0.997	0.094	1
3-3.8	0.038	12663	0.999	0.041	1
3.8-4.7	0.026	5817	0.999	0.028	1
4.7-5.1	0.024	1403	0.999	0.026	1
5.1-8	0.024	3808	1	0.026	1
8-12	0.021	960	1	0.023	1
12-50	0.024	409	1	0.026	1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→48.98 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1771	4968	5.09 %
R_work	0.1535	-	-
obs	0.1547	97573	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→48.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6532	0	115	394	7041

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019
X-RAY DIFFRACTION	f_angle_d	1.847
X-RAY DIFFRACTION	f_dihedral_angle_d	15.356	2538
X-RAY DIFFRACTION	f_chiral_restr	0.093	989
X-RAY DIFFRACTION	f_plane_restr	0.014	1206

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 (%)
1.9-1.92	0.3428	170	0.2918	3026	X-RAY DIFFRACTION	98
1.92-1.95	0.2604	161	0.2527	3073	X-RAY DIFFRACTION	100
1.95-1.97	0.2516	180	0.2406	3047	X-RAY DIFFRACTION	100
1.97-1.99	0.241	163	0.2259	3057	X-RAY DIFFRACTION	100
1.99-2.02	0.2521	146	0.2142	3098	X-RAY DIFFRACTION	100
2.02-2.05	0.2602	179	0.2123	3057	X-RAY DIFFRACTION	100
2.05-2.08	0.2505	167	0.1989	3091	X-RAY DIFFRACTION	100
2.08-2.11	0.2171	148	0.1879	3091	X-RAY DIFFRACTION	100
2.11-2.14	0.1911	159	0.1818	3075	X-RAY DIFFRACTION	100
2.14-2.18	0.2165	184	0.1781	3076	X-RAY DIFFRACTION	100
2.18-2.21	0.2197	168	0.1683	3052	X-RAY DIFFRACTION	100
2.21-2.25	0.2155	137	0.1697	3109	X-RAY DIFFRACTION	100
2.25-2.3	0.2136	168	0.166	3071	X-RAY DIFFRACTION	100
2.3-2.34	0.1868	171	0.1627	3109	X-RAY DIFFRACTION	100
2.34-2.4	0.1978	184	0.1584	3012	X-RAY DIFFRACTION	100
2.4-2.45	0.2083	185	0.1616	3100	X-RAY DIFFRACTION	100
2.45-2.51	0.1705	186	0.159	3065	X-RAY DIFFRACTION	100
2.51-2.58	0.2077	162	0.164	3089	X-RAY DIFFRACTION	100
2.58-2.66	0.2061	155	0.1625	3085	X-RAY DIFFRACTION	100
2.66-2.74	0.1852	171	0.154	3102	X-RAY DIFFRACTION	100
2.74-2.84	0.1899	145	0.1575	3094	X-RAY DIFFRACTION	100
2.84-2.95	0.1777	167	0.1545	3096	X-RAY DIFFRACTION	100
2.95-3.09	0.1596	154	0.1494	3108	X-RAY DIFFRACTION	100
3.09-3.25	0.1769	168	0.1563	3109	X-RAY DIFFRACTION	100
3.25-3.45	0.1843	156	0.1419	3088	X-RAY DIFFRACTION	100
3.45-3.72	0.1747	150	0.1364	3112	X-RAY DIFFRACTION	100
3.72-4.09	0.1473	166	0.1316	3113	X-RAY DIFFRACTION	100
4.09-4.69	0.1453	182	0.1233	3109	X-RAY DIFFRACTION	100
4.69-5.9	0.1556	173	0.148	3109	X-RAY DIFFRACTION	100
5.91-48.98	0.1396	163	0.1444	3182	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	1.0399	0.0715	0.0351	1.3619	-0.0478	1.0836	0.0488	0.076	0.1842	-0.0772	-0.063	0.1706	-0.2727	-0.1206	0.0072	0.2768	0.039	-0.0055	0.242	0.0128	0.2625	54.983	-15.7939	15.7117
2	6.7972	0.3583	1.388	1.429	-0.7954	1.8219	-0.0059	0.0414	0.232	-0.1484	-0.0438	-0.105	-0.2645	0.0923	0.0557	0.3664	0.0106	0.0437	0.2434	0.0175	0.2229	73.9228	-11.1816	5.4962
3	2.0367	0.4093	1.0547	1.5445	0.3116	2.0056	0.0094	0.1231	-0.0229	-0.0148	-0.0352	-0.2358	-0.116	0.2453	0.0237	0.2198	-0.0053	0.0258	0.2162	0.0318	0.2221	76.5547	-21.8675	19.7332
4	5.0851	-1.0062	-2.9962	1.7701	0.06	4.3672	-0.262	-0.4463	-0.747	0.4856	-0.0988	-0.0351	0.6484	-0.1054	0.3584	0.4869	-0.0461	-0.0467	0.4589	0.2106	0.5111	53.9547	-59.4857	44.234
5	1.2252	0.6413	-0.3512	1.0131	-0.3826	1.1969	0.0321	-0.1498	-0.3201	0.0711	-0.1038	-0.1754	0.1557	0.0668	0.0653	0.2638	-0.0019	-0.0317	0.2646	0.0365	0.3554	56.4326	-48.1531	27.9629
6	2.4765	0.4348	-0.0965	5.6642	-0.6919	3.0268	0.1771	-0.6871	-0.0516	0.7678	-0.2151	0.3561	-0.1171	-0.1747	0.0348	0.2894	-0.084	0.0114	0.4229	0.0086	0.2568	44.8425	-42.044	45.2348
7	0.776	0.5669	-0.01	3.4048	2.3928	4.9579	0.0985	-0.0934	-0.0238	0.1155	-0.2314	0.3472	-0.2079	-0.5025	0.1301	0.1859	0.0162	0.0005	0.2806	0.0162	0.27	43.1059	-34.9262	29.4415
8	4.0149	-4.7076	1.5141	6.0688	-0.2918	4.5141	-0.0969	-1.3378	0.2649	1.0971	0.1928	0.1684	-0.3647	-0.2542	-0.1015	0.6931	-0.205	0.0714	0.6503	-0.0724	0.4825	47.9535	-31.2333	50.7289

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 196 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 197 through 285 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 286 through 443 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 26 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 27 through 231 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 232 through 277 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 278 through 355 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 356 through 387 )

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3-methylbenzoyl-CoA reductase ... , 2 types, 2 molecules AB

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Non-polymers , 5 types, 405 molecules

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-Non-polymers , 5 types, 405 molecules

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3-methylbenzoyl-CoA reductase ... , 2 types, 2 molecules AB

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Non-polymers , 5 types, 405 molecules

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