PDB-9fsg: 25-hydroxy steroid kinase (25-HSK) + 25-OH-cholest-1,4-diene-3-one

ID or keywords:

Entry

Database: PDB / ID: 9fsg

Title

25-hydroxy steroid kinase (25-HSK) + 25-OH-cholest-1,4-diene-3-one

Components

Aminoglycoside phosphotransferase-like protein

Keywords

TRANSFERASE / anaerobic cholesterin degradation / ATP / cholest-1 / 4-diene-3-one / substrate-induced dimerisation

Function / homology

Acyl-CoA dehydrogenase family member 10/11, N-terminal / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / : / Aminoglycoside phosphotransferase-like protein

Function and homology information

Biological species

Sterolibacterium denitrificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Ermler, U. / Boll, M. / Demmer, U. / Warkentin, E.

Funding support

1items

Citation

Journal: To Be Published
Title: X-ray structure of 25-hydroxy steroid kinase (25-HSK)
Authors: Jacoby, C. / Demmer, U. / Warkentin, E. / Ermler, U. / Boll, M.

History

Deposition	Jun 21, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 14, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fsg.cif.gz	321.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9fsg.ent.gz		Display	PDB format
PDBx/mmJSON format	9fsg.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/fs/9fsg ftp://data.pdbj.org/pub/pdb/validation_reports/fs/9fsg	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
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (2)

Deposited unit

A: Aminoglycoside phosphotransferase-like protein

B: Aminoglycoside phosphotransferase-like protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	54.130, 100.470, 140.270
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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Protein , 1 types, 2 molecules AB

#1: Protein	Aminoglycoside phosphotransferase-like protein Mass: 43209.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sterolibacterium denitrificans (bacteria) Gene: SDENCHOL_21286 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A7Z7HU23

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Non-polymers , 5 types, 216 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-A1IF2 / 25-OH-cholest-1,4-diene-3-one / (8S,9S,10R,13R,14S,17R)-10,13-dimethyl-17-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-one Mass: 398.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₄₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.21 Å³/Da / Density % sol: 44.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, MES pH 6.5, zinc 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: Sep 13, 2021

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 101555 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.051 / Net I/σ(I): 15.99

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.6-1.7	1.837	16658	0.542	2.027	1
1.7-1.9	0.679	23830	0.889	0.754	1
1.9-2.2	0.186	21443	0.99	0.206	1
2.2-2.6	0.067	15397	0.997	0.075	1
2.6-3	0.042	8333	0.998	0.046	1
3-3.9	0.033	8509	0.999	0.037	1
3.9-4.7	0.028	3066	0.999	0.031	1
4.7-5.9	0.026	2082	0.999	0.029	1
5.9-8	0.025	1306	0.999	0.028	1
8-12	0.02	640	1	0.022	1
12-50	0.022	291	0.999	0.025	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: 1.6→40.84 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2383	5077	5 %
R_work	0.2058	-	-
obs	0.2074	101446	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→40.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6024	0	74	203	6301

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006
X-RAY DIFFRACTION	f_angle_d	0.926
X-RAY DIFFRACTION	f_dihedral_angle_d	18.283	2397
X-RAY DIFFRACTION	f_chiral_restr	0.054	884
X-RAY DIFFRACTION	f_plane_restr	0.008	1143

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 (%)
1.6-1.62	0.4091	169	0.3699	3137	X-RAY DIFFRACTION	100
1.62-1.64	0.3584	166	0.3345	3203	X-RAY DIFFRACTION	100
1.64-1.66	0.341	184	0.3199	3159	X-RAY DIFFRACTION	100
1.66-1.68	0.3545	165	0.3173	3190	X-RAY DIFFRACTION	100
1.68-1.7	0.3458	152	0.2898	3163	X-RAY DIFFRACTION	100
1.7-1.72	0.3332	175	0.2849	3160	X-RAY DIFFRACTION	100
1.72-1.75	0.2968	171	0.2758	3201	X-RAY DIFFRACTION	100
1.75-1.77	0.3237	164	0.265	3172	X-RAY DIFFRACTION	100
1.77-1.8	0.3032	179	0.2736	3215	X-RAY DIFFRACTION	100
1.8-1.83	0.3266	161	0.2572	3154	X-RAY DIFFRACTION	100
1.83-1.86	0.2851	160	0.2666	3212	X-RAY DIFFRACTION	100
1.86-1.9	0.285	160	0.2531	3198	X-RAY DIFFRACTION	100
1.9-1.93	0.2938	176	0.2374	3184	X-RAY DIFFRACTION	100
1.93-1.97	0.2753	177	0.2308	3172	X-RAY DIFFRACTION	100
1.97-2.02	0.2875	170	0.2291	3185	X-RAY DIFFRACTION	100
2.02-2.06	0.2987	160	0.2305	3193	X-RAY DIFFRACTION	100
2.06-2.11	0.244	176	0.2262	3196	X-RAY DIFFRACTION	100
2.11-2.17	0.27	182	0.2306	3210	X-RAY DIFFRACTION	100
2.17-2.24	0.2509	169	0.2208	3204	X-RAY DIFFRACTION	100
2.24-2.31	0.2831	157	0.2083	3200	X-RAY DIFFRACTION	100
2.31-2.39	0.2621	187	0.2188	3210	X-RAY DIFFRACTION	100
2.39-2.49	0.2776	185	0.2216	3176	X-RAY DIFFRACTION	100
2.49-2.6	0.2474	172	0.2205	3229	X-RAY DIFFRACTION	100
2.6-2.74	0.2464	162	0.2166	3241	X-RAY DIFFRACTION	100
2.74-2.91	0.252	169	0.2264	3215	X-RAY DIFFRACTION	100
2.91-3.13	0.2687	150	0.2213	3284	X-RAY DIFFRACTION	100
3.13-3.45	0.241	167	0.204	3256	X-RAY DIFFRACTION	100
3.45-3.94	0.2001	164	0.1759	3282	X-RAY DIFFRACTION	99
3.95-4.97	0.1706	174	0.1566	3304	X-RAY DIFFRACTION	99
4.97-40.84	0.1914	174	0.1754	3464	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	3.0294	0.9065	-0.6407	3.517	-2.6616	5.156	0.1111	-0.1174	-0.2695	0.0841	0.0268	0.3402	0.3515	-0.4539	-0.1585	0.305	-0.0036	0.0298	0.3169	-0.0329	0.3763	3.1868	9.1732	0.9381
2	1.9159	-0.797	0.4989	8.5602	-1.5474	2.179	0.0513	-0.0681	0.0971	-0.4528	0.0575	0.124	0.0414	-0.0527	-0.1235	0.1925	0.0093	-0.015	0.2622	-0.0206	0.2446	9.3024	12.2058	-8.6614
3	4.4643	-0.5718	-1.5943	1.4622	-0.0787	2.215	0.1512	-0.0893	0.29	-0.0221	-0.0069	-0.0643	-0.2405	-0.0171	-0.1299	0.2839	-0.0159	-0.0107	0.1788	-0.0278	0.2261	18.8312	11.8467	-4.2875
4	1.0905	0.4413	0.1124	1.1835	0.8735	6.0897	-0.0036	0.1721	-0.0417	-0.1603	0.1529	-0.0325	-0.0755	0.1329	-0.1602	0.156	0.0494	-0.0399	0.2005	-0.0388	0.2531	29.9699	0.0007	-13.7971
5	1.2205	0.2014	-0.3658	3.0518	-0.4533	2.4071	0.0142	-0.1898	-0.1692	0.3988	0.0228	-0.1335	0.517	0.208	-0.046	0.3694	0.0443	-0.0506	0.2267	0.0007	0.2223	26.5336	-14.1171	0.0716
6	0.8537	0.3106	0.1704	1.1045	0.1874	1.6462	0.0491	0.0955	-0.1456	-0.0103	0.1176	-0.1182	0.1938	0.1914	-0.1643	0.2837	0.0253	-0.0361	0.2818	-0.0327	0.3116	28.4532	-7.1726	-13.695
7	2.276	-0.8107	-0.8111	2.3475	0.5344	3.249	-0.0994	0.6829	-0.3408	-0.0023	0.1033	-0.0354	0.3339	-0.1715	0.009	0.6027	-0.0168	-0.0509	0.261	-0.0212	0.3704	21.3473	-23.641	-13.1329
8	4.8952	1.3468	-1.0786	4.4888	-0.3714	4.6883	0.2165	0.1128	0.3427	-0.051	0.1785	-0.2574	-0.3489	0.4634	-0.3117	0.2249	-0.0386	0.0007	0.3841	-0.0842	0.345	30.8611	-3.348	-48.9596
9	1.0655	-0.0436	0.5473	0.7864	0.2031	0.947	0.0087	0.0868	0.0324	0.0482	-0.0153	-0.072	-0.0457	0.0491	-0.0394	0.2504	-0.0027	-0.0339	0.2601	0.0061	0.2917	12.1594	-6.7616	-43.4306
10	1.2687	-0.4585	0.2902	1.5895	-0.2679	1.7937	0.0398	-0.0259	-0.1374	0.019	0.0038	-0.0479	0.2074	-0.0829	-0.051	0.2388	-0.0103	-0.047	0.2485	-0.0234	0.2575	4.9508	-17.8339	-39.2674
11	1.0816	-0.1865	1.5176	1.1606	-0.3304	2.0645	-0.0303	-0.0979	0.08	0.1353	-0.0266	-0.0198	0.0247	-0.1753	0.0038	0.2188	-0.0122	-0.0283	0.265	-0.0197	0.2761	2.9169	-12.7131	-30.4923
12	7.3818	-2.0753	1.165	6.6878	-0.8592	6.8273	-0.2335	-1.1072	-0.1044	0.6888	0.3947	0.1293	-0.146	-0.253	-0.1547	0.4328	-0.0186	-0.0076	0.403	0.0314	0.2603	6.9076	-25.0724	-22.4138

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 136 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 137 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 246 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 247 through 347 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 348 through 379 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 8 through 78 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 193 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 194 through 270 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 271 through 347 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 348 through 379 )

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