PDB-8s1t: BzdNO-cyclohexa-1,5-diene-1-carboxy-CoA complex

ID or keywords:

Entry

Database: PDB / ID: 8s1t

Title

BzdNO-cyclohexa-1,5-diene-1-carboxy-CoA complex

Components

BzdN
BzdO

Keywords

OXIDOREDUCTASE / Benzoyl-CoA reductase / reductive dearomatization / iron-sulfur clusters

Function / homology

Function and homology information

iron-sulfur cluster binding / metal ion binding
Similarity search - Function

Biological species

Azoarcus sp. CIB (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

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

Funding support

1items

Citation

Journal: To Be Published
Title: X-ray structure of the BzdNO-benzoyl-CoA complex
Authors: Ermler, U. / Boll, M. / Fuchs, J. / Demmer, U.

History

Deposition	Feb 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s1t.cif.gz	953.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8s1t.ent.gz	807.7 KB	Display	PDB format
PDBx/mmJSON format	8s1t.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/s1/8s1t ftp://data.pdbj.org/pub/pdb/validation_reports/s1/8s1t	HTTPS FTP

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Related structure data

Related structure data	8s02C 8s2rC 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: BzdO

B: BzdN

C: BzdO

D: BzdN

hetero molecules

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

1

A: BzdO

B: BzdN

hetero molecules

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

2

C: BzdO

D: BzdN

hetero molecules

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

Unit cell

Length a, b, c (Å)	208.210, 102.750, 86.820
Angle α, β, γ (deg.)	90.00, 102.40, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-839- HOH

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Protein , 2 types, 4 molecules ACBD

#1: Protein	BzdO Mass: 51272.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus sp. CIB (bacteria) / Gene: bzdO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q68VL9
#2: Protein	BzdN Mass: 43482.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus sp. CIB (bacteria) / Gene: bzdN / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q68VM0

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Non-polymers , 6 types, 915 molecules

#3: Chemical	ChemComp-4KX / 1,5 Dienoyl-CoA / Cyclohex-1,5-diene-1-carbonyl-CoA Mass: 873.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₈H₄₂N₇O₁₇P₃S
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: 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
#7: Chemical	ChemComp-BJ8 / Double cubane cluster Mass: 735.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₈S₉
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 905 / Source method: isolated from a natural source / Formula: H₂O / Feature type: SUBJECT OF INVESTIGATION

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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: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG3350, BTP, 200 mM formate or acetate

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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: Apr 11, 2023

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.45→50 Å / Num. obs: 310096 / % possible obs: 98.5 % / Redundancy: 20.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.072 / Net I/σ(I): 10.25

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.45-1.55	1.106	54697	0.562	1.331	1
1.55-1.75	0.429	78180	0.864	0.51	1
1.75-2.05	0.163	66805	0.977	0.195	1
2.05-2.55	0.071	52541	0.993	0.085	1
2.55-3.5	0.04	35390	0.997	0.048	1
3.5-4.6	0.029	12461	0.997	0.035	1
4.6-5.7	0.027	4707	0.998	0.033	1
5.7-8	0.029	3376	0.998	0.034	1
8-12	0.025	1359	0.999	0.03	1
12-50	0.03	580	0.998	0.036	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: 1.45→43.6 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2004	15598	5.04 %
R_work	0.182	-	-
obs	0.1829	309763	98.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→43.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13045	0	192	903	14140

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01
X-RAY DIFFRACTION	f_angle_d	1.789
X-RAY DIFFRACTION	f_dihedral_angle_d	5.596	1884
X-RAY DIFFRACTION	f_chiral_restr	0.078	1922
X-RAY DIFFRACTION	f_plane_restr	0.01	2426

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 (%)
1.45-1.47	0.3959	441	0.3895	8781	X-RAY DIFFRACTION	89
1.47-1.48	0.4273	486	0.4141	9533	X-RAY DIFFRACTION	96
1.48-1.5	0.3401	546	0.3207	9900	X-RAY DIFFRACTION	99
1.5-1.52	0.4047	547	0.3744	9594	X-RAY DIFFRACTION	97
1.52-1.54	0.3647	523	0.374	9534	X-RAY DIFFRACTION	96
1.54-1.56	0.3055	543	0.276	9937	X-RAY DIFFRACTION	100
1.56-1.58	0.2889	508	0.2572	9898	X-RAY DIFFRACTION	100
1.58-1.61	0.2638	567	0.2451	9903	X-RAY DIFFRACTION	100
1.61-1.63	0.2663	525	0.2363	9935	X-RAY DIFFRACTION	100
1.63-1.66	0.253	518	0.2226	9954	X-RAY DIFFRACTION	100
1.66-1.69	0.2503	511	0.2043	9842	X-RAY DIFFRACTION	100
1.69-1.72	0.2384	552	0.2097	9877	X-RAY DIFFRACTION	99
1.72-1.75	0.239	542	0.1964	9873	X-RAY DIFFRACTION	100
1.75-1.79	0.2152	499	0.1835	9980	X-RAY DIFFRACTION	100
1.79-1.83	0.2119	515	0.1783	9864	X-RAY DIFFRACTION	100
1.83-1.87	0.1998	528	0.1753	9975	X-RAY DIFFRACTION	100
1.87-1.92	0.2618	515	0.2054	9477	X-RAY DIFFRACTION	96
1.92-1.97	0.2202	503	0.1903	9754	X-RAY DIFFRACTION	98
1.97-2.03	0.1811	508	0.1612	9932	X-RAY DIFFRACTION	100
2.03-2.09	0.2117	511	0.1793	9396	X-RAY DIFFRACTION	95
2.09-2.17	0.1658	521	0.1514	10015	X-RAY DIFFRACTION	100
2.17-2.25	0.1893	506	0.1576	9613	X-RAY DIFFRACTION	97
2.25-2.36	0.1645	512	0.1551	9906	X-RAY DIFFRACTION	99
2.36-2.48	0.1782	483	0.1529	9982	X-RAY DIFFRACTION	99
2.48-2.63	0.1664	524	0.1524	9935	X-RAY DIFFRACTION	99
2.63-2.84	0.1929	524	0.1632	9834	X-RAY DIFFRACTION	99
2.84-3.12	0.187	510	0.1715	10011	X-RAY DIFFRACTION	100
3.12-3.58	0.1876	522	0.1742	9943	X-RAY DIFFRACTION	99
3.58-4.5	0.1578	550	0.1565	9911	X-RAY DIFFRACTION	99
4.5-43.6	0.1912	558	0.1789	10076	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	2.8256	-2.7384	3.0017	6.3714	-5.2786	7.812	0.1139	0.3543	-0.0915	-0.6852	-0.0506	0.0762	0.4409	-0.0302	-0.0605	0.2547	-0.0424	0.0372	0.2064	-0.0351	0.141	32.1357	-4.1734	-7.3931
2	3.4416	0.5774	1.4182	1.494	-0.078	0.8287	-0.0165	0.1776	-0.183	-0.1516	0.0203	-0.2041	0.0728	0.1054	-0.0041	0.1775	-0.0032	0.0359	0.1422	0.0023	0.1212	39.5755	-8.6549	10.2183
3	0.7158	0.691	0.2586	2.2362	0.3808	0.6512	0.0086	0.033	-0.0755	-0.0332	0.0187	-0.0291	0.0473	0.0324	-0.0276	0.1627	0.0085	0.0115	0.1417	0.0068	0.1379	28.2058	-10.7389	16.9279
4	3.2832	-3.4032	-1.461	5.1622	1.5509	2.1261	-0.0408	-0.1836	0.2803	0.0562	0.1355	-0.5039	-0.0166	0.2438	-0.112	0.1195	-0.0226	-0.006	0.1527	-0.0121	0.1466	44.6716	1.8336	23.2753
5	1.2211	-0.3831	0.8162	0.6206	0.053	1.4514	-0.022	0.1471	0.0326	-0.1603	-0.011	-0.0451	-0.0374	0.0415	0.0412	0.2157	-0.0221	0.0378	0.1394	0.0114	0.1394	30.9024	7.2555	1.0802
6	1.3075	-0.3811	0.6121	0.9844	-0.1845	1.3486	-0.0687	-0.0486	0.0946	0.0448	0.0055	0.0919	-0.1465	-0.0733	0.06	0.1981	0.0051	0.0052	0.1748	-0.0124	0.1775	16.7836	9.5393	10.5474
7	4.2012	-3.9855	3.1177	5.9909	-3.7916	3.8142	0.0534	0.1418	0.1254	-0.2908	-0.0443	0.0145	0.1024	-0.0577	-0.0399	0.1405	-0.0142	0.0196	0.1661	-0.0257	0.1531	5.2116	3.7236	-0.427
8	2.31	-1.6153	0.7073	6.5177	-2.98	4.7924	-0.0214	-0.2573	0.017	0.4399	0.2775	0.6589	-0.0146	-0.6629	-0.2582	0.1979	0.0071	0.0658	0.33	-0.0377	0.1861	2.746	8.1781	49.3031
9	3.2138	1.2237	1.398	1.7811	0.7541	2.7531	-0.0541	0.0292	0.0867	-0.009	-0.0696	0.2207	-0.0265	-0.1334	0.1279	0.2047	0.0183	0.0341	0.1789	0.0006	0.1717	11.9481	9.7238	38.0127
10	1.9936	-1.4482	-1.5361	3.985	1.6862	3.9231	-0.0017	0.0722	-0.0773	-0.1323	-0.1132	0.2387	0.0049	-0.4107	0.1194	0.179	-0.0069	0.0026	0.1984	-0.0208	0.2076	6.4209	2.9921	24.1706
11	2.0097	-1.1389	-0.2199	2.1764	0.9876	2.1698	-0.0424	-0.0616	0.0463	0.0463	0.0026	0.1222	-0.0842	-0.1714	0.0427	0.182	0.008	0.0162	0.1626	0.0062	0.1524	11.8507	10.1958	29.6915
12	3.1853	-1.1632	1.1875	0.9273	-0.5644	0.6278	-0.0978	-0.0681	0.1177	0.126	0.0491	0.0261	-0.0681	-0.0275	0.0516	0.2108	0.0057	0.0136	0.1634	-0.0078	0.1489	23.1396	10.6126	31.4242
13	3.7393	-1.7054	0.6812	2.847	-1.6042	1.9132	0.0542	-0.0495	0.2882	0.2415	0.0162	-0.0405	-0.2727	-0.0306	-0.0816	0.1951	-0.0244	0.0066	0.1082	-0.0037	0.1235	27.6793	18.7529	38.5531
14	1.7062	1.2005	-0.6703	3.5227	-1.0494	1.7291	0.0436	-0.1147	-0.1024	0.3756	-0.055	-0.0102	0.1445	-0.1186	0.0032	0.2638	-0.0075	0.0328	0.1878	-0.0156	0.1047	16.4547	0.5446	51.7815
15	1.3702	-0.3388	-0.489	3.4176	1.2624	4.5514	-0.0145	-0.2146	-0.0413	0.4104	-0.0498	0.284	0.2561	-0.48	0.0527	0.1879	-0.0291	0.0334	0.2562	0.0011	0.164	10.1678	-5.5928	53.2801
16	0.6692	0.1605	0.4224	1.1534	0.5416	1.1249	0.0637	-0.1443	-0.1151	0.2339	-0.076	0.0911	0.2323	-0.1262	0.0123	0.2386	-0.0104	0.031	0.1497	0.0089	0.132	20.502	-6.6163	41.2139
17	5.9312	1.3356	-0.901	3.7927	-1.1495	2.9292	0.0315	-0.102	-0.4231	0.2513	0.0093	0.2951	0.6091	-0.3951	-0.0412	0.3713	-0.0879	0.0166	0.2032	-0.0426	0.1784	11.9375	-19.0785	34.5502
18	6.9945	5.4321	-4.4618	6.2526	-3.6581	5.0877	0.1869	-0.293	0.2624	0.5481	-0.0549	0.3722	-0.1484	-0.1259	-0.1329	0.2871	0.0473	0.0245	0.1721	-0.0036	0.1501	21.3464	-46.7592	40.71
19	4.6317	-0.4952	0.4275	1.2898	-0.5761	0.4769	-0.0627	-0.2175	0.2125	0.1876	-0.0065	-0.1062	-0.1018	0.0355	0.0655	0.2213	0.0017	-0.0019	0.1358	0.0023	0.1157	35.7111	-42.1781	27.8969
20	1.0592	-0.7588	-0.1244	2.1397	0.0017	0.627	-0.0098	-0.0448	0.0861	0.0697	0.0223	-0.0061	-0.0371	-0.0152	-0.0093	0.1827	-0.004	0.0056	0.14	0.0088	0.1384	28.2217	-39.68	17.0235
21	2.9269	3.6034	2.4349	6.0024	4.3001	5.067	0.0202	0.0577	-0.1259	0.1162	0.145	-0.3415	0.096	0.2683	-0.1827	0.1434	0.0359	-0.0053	0.1446	-0.0012	0.1478	45.7941	-52.7182	18.1911
22	1.2846	0.3528	-0.1659	0.6554	0.1207	0.6747	-0.0149	-0.1332	-0.0861	0.1909	-0.0035	0.0497	0.0789	-0.0578	0.0204	0.2488	0.0055	0.0212	0.121	0.0191	0.1383	23.5574	-58.9604	30.4584
23	1.9489	1.1146	0.0647	3.817	-1.3172	1.6072	0.085	-0.1643	0.1038	0.4069	0.028	0.6929	-0.0705	-0.467	-0.1113	0.2368	-0.0206	0.0539	0.2695	-0.0194	0.243	5.4042	-53.23	20.6247
24	3.7378	3.1306	-2.1862	9.1832	-3.7314	4.8442	-0.1036	0.5532	0.1211	-0.8135	0.343	0.6836	0.2016	-0.7309	-0.2459	0.2495	0.0162	-0.0671	0.3799	-0.0499	0.1716	19.0897	-58.6537	-23.3394
25	4.5398	-2.0192	0.2262	2.4199	-0.1855	0.976	0.017	0.0887	-0.1518	-0.0669	-0.0807	0.1696	0.0301	-0.1575	0.0714	0.2259	-0.026	0.0068	0.1808	-0.0044	0.1366	21.8192	-60.4103	-8.817
26	1.1475	0.154	-0.0424	0.5813	0.1528	0.659	-0.0047	0.0594	-0.1136	-0.0514	-0.0108	0.0938	0.0872	-0.1568	0.0179	0.2226	-0.0194	-0.0043	0.196	0.0031	0.1781	19.8564	-59.155	0.1862
27	5.3183	3.6342	0.5127	5.4167	0.2029	1.6533	0.0593	0.1153	-0.2752	-0.1324	-0.0032	-0.1964	0.2867	0.0289	-0.0849	0.174	0.0208	0.0121	0.1054	0.0119	0.1233	36.9418	-69.5706	-2.8613
28	1.1979	-0.8893	0.4392	3.6585	-1.4578	1.4654	0.1399	0.1863	0.122	-0.3721	-0.1039	-0.169	-0.0987	-0.0658	-0.0255	0.2574	0.0177	0.0391	0.1946	-0.0045	0.1085	32.4102	-51.1863	-19.7941
29	1.3279	-0.346	-0.7559	2.6371	0.2546	4.2727	0.1497	0.4249	0.0969	-0.4936	-0.0968	0.0718	-0.2835	-0.4572	-0.0564	0.2543	0.0319	-0.0112	0.2847	0.0286	0.1634	27.2343	-45.2781	-23.6142
30	1.0907	-0.4571	-0.5573	1.3279	0.5197	0.8194	0.103	0.1813	0.1612	-0.2206	-0.0582	-0.0111	-0.2247	-0.0799	-0.0399	0.2332	0.0089	0.022	0.1485	0.0177	0.1342	31.5159	-44.2352	-8.3013
31	4.9457	-1.0438	1.2081	3.7618	-2.2359	4.4648	0.0999	0.3093	0.3643	-0.2464	0.133	0.205	-0.6929	-0.4852	-0.1914	0.3926	0.111	0.0637	0.2369	-0.0059	0.219	20.9572	-31.8591	-5.9347

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 160 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 161 through 187 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 188 through 343 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 344 through 397 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 398 through 442 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 27 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 63 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 84 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 85 through 113 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 114 through 133 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 134 through 158 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 159 through 206 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 207 through 243 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 244 through 327 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 328 through 376 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 6 through 31 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 32 through 72 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 73 through 160 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 161 through 187 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 188 through 366 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 367 through 436 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 2 through 27 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 28 through 63 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 64 through 133 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 134 through 158 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 159 through 206 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 207 through 243 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 244 through 327 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 328 through 376 )

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