PDB-8vwr: Structure of steroid hydratase from Comamonas testosteroni

ID or keywords:

Entry

Database: PDB / ID: 8vwr

Title

Structure of steroid hydratase from Comamonas testosteroni

Components

Acyl dehydratase

Keywords

LYASE / Enoyl-CoA hydratase / MaoC / Hot dog fold / Bile acid catabolism

Function / homology

Function and homology information

Nodulation protein N-like / Domain of unknown function DUF35, OB-fold, C-terminal / DUF35 OB-fold domain, acyl-CoA-associated / Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / Rubredoxin-like zinc ribbon domain (DUF35_N) / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology

Biological species

Comamonas testosteroni KF-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Schroeter, K.L. / Forrester, T.J.B. / Kimber, M.S. / Seah, S.Y.K.

Funding support

Canada, 2items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Shy is a proteobacterial steroid hydratase which catalyzes steroid side chain degradation without requiring a catalytically inert partner domain.
Authors: Schroeter, K.L. / Rolfe, N. / Forrester, T.J.B. / Kimber, M.S. / Seah, S.Y.K.

History

Deposition	Feb 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 31, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vwr.cif.gz	198.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8vwr.ent.gz	163.4 KB	Display	PDB format
PDBx/mmJSON format	8vwr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vwr_validation.pdf.gz	456.7 KB	Display	wwPDB validaton report
Full document	8vwr_full_validation.pdf.gz	459.1 KB	Display
Data in XML	8vwr_validation.xml.gz	14.6 KB	Display
Data in CIF	8vwr_validation.cif.gz	19.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vw/8vwr ftp://data.pdbj.org/pub/pdb/validation_reports/vw/8vwr	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.11406128 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Acyl dehydratase

B: Acyl dehydratase

hetero molecules

35.8 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)	95.280, 95.280, 98.590
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

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Protein , 1 types, 2 molecules AB

#1: Protein	Acyl dehydratase Mass: 17439.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: CtesDRAFT_PD3653 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR / References: UniProt: B7X4S7

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Non-polymers , 5 types, 105 molecules

#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.42 Å³/Da / Density % sol: 64 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1 mcL of reservoir solution (0.1 M sodium cacodylate, 0.2 M calcium acetate hydrate, 40% PEG 300) combined with 1 mcL 30 mM acetyl-CoA and 1 mcL of 20 mg/ml protein

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 9, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 2.05→47.64 Å / Num. obs: 32918 / % possible obs: 99.96 % / Redundancy: 20 % / B_iso Wilson estimate: 49.72 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.1249 / R_pim(I) all: 0.02869 / R_rim(I) all: 0.1282 / Net I/σ(I): 13.81
Reflection shell	Resolution: 2.05→2.123 Å / Redundancy: 21.1 % / R_merge(I) obs: 3.193 / Mean I/σ(I) obs: 1 / Num. unique obs: 3235 / CC_1/2: 0.492 / CC star: 0.917 / R_pim(I) all: 0.7095 / R_rim(I) all: 3.272 / % possible all: 99.97

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Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→47.64 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2236	1648	5 %
R_work	0.1971	-	-
obs	0.1984	32909	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.05→47.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2452	0	60	96	2608

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2551
X-RAY DIFFRACTION	f_angle_d	0.547	3438
X-RAY DIFFRACTION	f_dihedral_angle_d	13.665	969
X-RAY DIFFRACTION	f_chiral_restr	0.048	384
X-RAY DIFFRACTION	f_plane_restr	0.005	444

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 (%)
2.05-2.08	0.4034	139	0.3424	2728	X-RAY DIFFRACTION	100
2.08-2.12	0.3465	145	0.3133	2711	X-RAY DIFFRACTION	100
2.12-2.15	0.3046	133	0.297	2695	X-RAY DIFFRACTION	100
2.15-2.19	0.3213	147	0.2846	2703	X-RAY DIFFRACTION	100
2.19-2.23	0.3219	145	0.2818	2740	X-RAY DIFFRACTION	100
2.23-2.28	0.3078	137	0.2661	2675	X-RAY DIFFRACTION	100
2.28-2.33	0.2901	144	0.2566	2745	X-RAY DIFFRACTION	100
2.33-2.38	0.3152	131	0.2561	2735	X-RAY DIFFRACTION	100
2.38-2.44	0.2863	152	0.2471	2721	X-RAY DIFFRACTION	100
2.44-2.51	0.2397	143	0.2417	2666	X-RAY DIFFRACTION	100
2.51-2.58	0.2354	142	0.2188	2746	X-RAY DIFFRACTION	100
2.58-2.67	0.2689	129	0.2014	2700	X-RAY DIFFRACTION	100
2.67-2.76	0.2555	148	0.1996	2692	X-RAY DIFFRACTION	100
2.76-2.87	0.2316	143	0.2046	2728	X-RAY DIFFRACTION	100
2.87-3	0.2862	149	0.2249	2729	X-RAY DIFFRACTION	100
3-3.16	0.2704	137	0.2402	2708	X-RAY DIFFRACTION	100
3.16-3.36	0.2508	151	0.197	2693	X-RAY DIFFRACTION	100
3.36-3.62	0.1979	142	0.1866	2704	X-RAY DIFFRACTION	100
3.62-3.98	0.1889	151	0.1844	2714	X-RAY DIFFRACTION	100
3.98-4.56	0.1529	138	0.1503	2729	X-RAY DIFFRACTION	100
4.56-5.74	0.1876	146	0.1562	2696	X-RAY DIFFRACTION	100
5.74-47.64	0.2209	146	0.1952	2712	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	7.3032	0.9745	1.6039	5.3786	-0.779	5.9211	-0.3262	0.6129	1.5077	-1.1962	-0.1174	0.5442	-1.1208	-0.0097	0.4406	1.211	0.0305	-0.3392	0.8084	0.2981	1.0797	26.8278	1.253	-22.3914
2	2.872	0.7336	0.0637	6.0765	-1.7782	3.7886	-0.0701	0.1671	0.2548	0.0069	-0.0099	-0.3798	-0.1382	0.1189	0.1328	0.435	-0.0599	0.0014	0.3098	0.0032	0.4665	45.5815	-8.2609	2.1262
3	4.7941	-5.3988	6.3211	6.0859	-7.0943	8.2589	-0.0995	0.2419	1.1008	0.6731	-0.4776	-1.2563	-0.0212	1.4586	0.6563	0.6252	-0.0105	-0.0879	0.6415	-0.0303	0.8762	58.4553	-12.6741	7.8381
4	5.494	-0.6783	2.3876	3.3837	2.187	3.4548	-0.0003	0.0034	-0.2224	-0.0152	0.2527	0.413	-0.0745	-0.1813	-0.3084	0.4659	-0.0513	-0.0195	0.4058	0.0693	0.5588	40.5413	-8.3826	-0.1354
5	5.3847	2.9426	6.104	3.8591	3.0154	6.9708	-0.6022	-0.1125	1.6436	-0.9242	-0.2746	1.7563	-0.8793	-0.6367	1.0206	0.8145	0.1296	-0.1635	0.5561	0.0053	1.0856	28.5943	1.6923	-12.1038
6	3.9775	-2.8609	1.9118	3.6437	0.6134	3.347	0.4213	-0.4784	-0.2185	0.7421	-0.4729	0.9261	-0.3729	-1.1864	0.312	0.7295	-0.0201	0.0412	0.7282	0.0313	0.8075	28.5591	-11.8201	-11.4415
7	4.2068	2.862	3.768	5.2496	4.9826	9.1743	0.1015	0.3019	-0.0848	-0.0765	0.3142	-0.4289	0.1183	0.2418	-0.3827	0.5354	-0.1324	0.0285	0.3941	0.0424	0.5992	48.9321	-9.0078	-4.5027
8	6.5468	1.942	3.5544	4.0463	2.6512	3.4909	-0.3045	1.182	0.4382	-0.8054	0.0226	0.1613	-0.4105	0.9311	0.1724	0.7787	-0.0822	-0.0708	0.5817	0.0871	0.5284	38.0425	-4.3166	-15.9412
9	4.8198	1.5911	4.7721	4.7342	4.1428	6.3686	-0.0769	-0.054	0.1955	-0.4187	-0.0783	0.3742	-0.4243	-0.1925	0.1417	0.7374	-0.1191	-0.0566	0.4396	0.0851	0.5125	36.4948	-7.718	-14.3148
10	3.9089	3.3778	3.8262	3.0803	3.1734	3.7985	0.1973	1.1984	-0.211	-0.5541	0.1569	-2.274	-0.5458	1.1054	-0.3312	0.6419	-0.1547	0.0676	0.5662	-0.0329	0.7218	53.0744	-1.6787	-6.6848
11	3.8036	1.0042	4.8321	5.5432	2.3594	6.1298	-0.49	0.5945	-0.4921	-0.7039	0.0673	0.6657	-0.5172	-0.0166	0.562	0.6162	0.0104	-0.0382	0.4414	0.0737	0.6155	33.8441	-9.4955	-13.2827
12	8.8465	0.7246	0.7729	7.1295	-0.7335	9.5434	-0.1012	0.2898	-0.9001	-0.1783	0.1573	-1.3781	0.961	1.8877	0.0952	0.674	0.1244	0.1068	0.7477	-0.1094	1.0883	55.8449	-37.1427	-11.438
13	5.1561	-0.8828	-4.1363	1.607	0.1881	5.9187	-0.1207	0.3234	-0.326	0.0363	-0.0309	0.0856	0.6168	-0.393	0.1044	0.4875	-0.1395	-0.0379	0.4111	-0.0055	0.4659	36.255	-32.7238	-2.361
14	6.4979	2.7402	0.6533	2.7042	2.4488	2.6751	-0.2744	-0.2148	1.0491	0.5202	0.09	1.2414	-0.5841	-0.6016	0.2057	0.5823	0.0231	0.0275	0.4907	-0.0229	0.7603	28.1393	-10.8893	5.4281
15	8.6701	-2.928	1.878	6.1044	3.77	8.0399	0.5314	-0.1637	0.8783	-0.2184	-0.5262	1.9245	-0.9454	-1.5157	-0.0507	0.6344	0.0099	-0.0548	0.8166	0.0561	1.219	18.0914	-14.0791	1.8555
16	2.7465	-3.6325	0.6463	4.8619	-0.2191	3.5209	-0.1726	-0.0358	0.0836	0.3368	0.253	0.2504	0.2512	-0.4612	-0.0591	0.5191	-0.0844	-0.0166	0.3918	0.0256	0.4869	37.1716	-20.5198	1.5653
17	9.6937	-2.2525	-5.0127	4.3707	-0.3843	6.4111	-0.2237	-0.0313	-0.0604	0.5195	-0.0336	-0.7453	0.6208	1.3139	0.1551	0.5288	-0.0038	-0.1213	0.742	0.061	0.6244	51.1596	-33.6729	-2.3296
18	5.2104	-0.9474	5.0611	4.4246	-3.7015	6.8631	-0.9305	0.6872	1.5265	1.0772	0.0717	-1.8286	-1.1337	1.9719	-0.0311	0.7421	-0.0225	-0.0819	0.7555	0.0556	0.9446	52.2086	-20.695	-6.8414
19	5.236	3.956	-3.3164	3.5831	-3.0782	8.2999	-0.0978	0.1831	-0.0032	-0.4559	0.3536	0.5844	0.4574	-0.4949	-0.3971	0.4584	-0.1235	-0.0484	0.4479	0.0073	0.6407	30.4201	-21.7563	-4.9499
20	7.513	-3.4309	-4.5256	4.8426	2.6963	3.7736	-0.0597	0.4007	-0.2415	-0.417	-0.1386	0.073	0.0988	0.2964	0.012	0.4859	-0.1323	-0.065	0.6089	-0.0036	0.3853	42.8582	-30.4871	-10.279
21	2.4011	-2.5559	-3.3286	4.1942	1.1797	8.6953	0.5054	0.1106	-0.0573	-0.3856	-0.1628	-0.7708	-0.7695	1.095	-0.2448	0.6186	-0.19	-0.0066	0.6168	0.0276	0.5583	45.8543	-26.0968	-10.5034
22	4.1973	2.8788	-3.8055	2.4806	-2.3286	3.5579	0.1601	1.0346	-0.4125	-0.8836	0.5477	1.7239	0.85	-1.7606	-0.8608	0.6012	-0.1536	-0.0955	0.6761	-0.0263	0.6521	26.6667	-29.6618	-5.6073
23	3.7722	-4.8247	-2.1307	6.9839	1.3376	4.741	0.4348	-0.067	1.3402	-0.0481	0.1027	-0.6996	0.3062	0.1538	-0.634	0.5876	-0.0913	-0.097	0.4139	-0.0332	0.5106	47.5307	-23.7804	-8.9549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 159 through 173 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 174 through 208 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 209 through 224 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 225 through 234 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 235 through 247 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 248 through 254 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 255 through 268 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 269 through 281 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 282 through 295 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 296 through 302 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 303 through 312 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 159 through 173 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 174 through 188 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 189 through 208 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 209 through 224 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 225 through 234 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 235 through 247 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 248 through 254 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 255 through 268 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 269 through 280 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 281 through 295 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 296 through 302 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 303 through 312 )

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