PDB-8ju4: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhod...

ID or keywords:

Entry

Database: PDB / ID: 8ju4

Title

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione

Components

3-ketosteroid dehydrogenase

Keywords

OXIDOREDUCTASE / 3-ketosteroid delta1-dehydrogenase / Rhodococcus erythropolis SQ1 / 1 / 4-androstadiene-3 / 17- dione

Function / homology

Function and homology information

3-oxosteroid 1-dehydrogenase / 3-oxosteroid 1-dehydrogenase activity / steroid metabolic process / nucleotide binding
Similarity search - Function

Biological species

Rhodococcus electrodiphilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Hu, Y.L. / Li, X. / Cheng, X.Y. / Song, S.K. / Su, Z.D.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
Authors: Song, S.K. / Hu, Y.L. / Su, Z.D.

History

Deposition	Jun 24, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ju4.cif.gz	190.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ju4.ent.gz	151 KB	Display	PDB format
PDBx/mmJSON format	8ju4.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/ju/8ju4 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/8ju4	HTTPS FTP

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Related structure data

Related structure data	8kczC 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
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (3) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: 3-ketosteroid dehydrogenase

hetero molecules

55.7 kDa, 1 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)	118.890, 118.890, 118.610
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	151
Space group name H-M	P3₁12

#1: Protein	3-ketosteroid dehydrogenase / 3-oxosteroid 1-dehydrogenase Mass: 54651.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus electrodiphilus (bacteria) / Gene: kstD1, BS297_24040, rerp_49010, RERY_47440 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RA02, 3-oxosteroid 1-dehydrogenase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-ANB / ANDROSTA-1,4-DIENE-3,17-DIONE Mass: 284.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.43 Å³/Da / Density % sol: 72.22 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 3, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.3→29.705 Å / Num. obs: 42707 / % possible obs: 99.9 % / Redundancy: 20.6 % / R_merge(I) obs: 0.107 / Net I/σ(I): 19.2
Reflection shell	Resolution: 2.3→2.36 Å / R_merge(I) obs: 1.584 / Num. unique obs: 3135

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→29.705 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.954 / WR_factor R_free: 0.215 / WR_factor R_work: 0.182 / Average fsc free: 0.8971 / Average fsc work: 0.9073 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2229	2164	5.071 %
R_work	0.1917	40509	-
all	0.193	-	-
obs	-	42673	99.92 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 53.403 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.172 Å²	0.586 Å²	-0 Å²
2-	-	1.172 Å²	0 Å²
3-	-	-	-3.802 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→29.705 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3842	0	74	4	3920

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	4000
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.017	3588
X-RAY DIFFRACTION	r_angle_refined_deg	1.716	1.641	5450
X-RAY DIFFRACTION	r_angle_other_deg	2.459	1.574	8314
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.874	5	522
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.846	22.304	204
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.741	15	581
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.129	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	517
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	4666
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	835
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	766
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.227	0.2	3274
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	1965
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1794
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	73
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.35	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.332	0.2	45
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.035	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.688	5.531	2091
X-RAY DIFFRACTION	r_mcbond_other	4.669	5.528	2090
X-RAY DIFFRACTION	r_mcangle_it	5.975	8.292	2612
X-RAY DIFFRACTION	r_mcangle_other	5.974	8.295	2613
X-RAY DIFFRACTION	r_scbond_it	6.623	6.024	1909
X-RAY DIFFRACTION	r_scbond_other	6.622	6.023	1910
X-RAY DIFFRACTION	r_scangle_it	9.034	8.805	2838
X-RAY DIFFRACTION	r_scangle_other	9.033	8.805	2839
X-RAY DIFFRACTION	r_lrange_it	13.369	65.085	4245
X-RAY DIFFRACTION	r_lrange_other	13.368	65.086	4246

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.3-2.36	0.312	167	0.286	2930	0.287	3097	0.82	0.825	100	0.275
2.36-2.424	0.295	161	0.279	2912	0.28	3076	0.843	0.851	99.9025	0.262
2.424-2.494	0.325	144	0.279	2801	0.282	2945	0.809	0.845	100	0.26
2.494-2.57	0.326	138	0.264	2728	0.267	2866	0.839	0.852	100	0.241
2.57-2.653	0.341	149	0.26	2641	0.264	2791	0.853	0.872	99.9642	0.231
2.653-2.746	0.259	117	0.242	2591	0.243	2708	0.899	0.891	100	0.214
2.746-2.848	0.273	135	0.242	2478	0.243	2613	0.88	0.9	100	0.212
2.848-2.964	0.268	118	0.226	2394	0.228	2515	0.912	0.919	99.8807	0.204
2.964-3.094	0.269	119	0.224	2279	0.226	2398	0.91	0.921	100	0.204
3.094-3.243	0.238	108	0.217	2200	0.218	2311	0.92	0.936	99.8702	0.204
3.243-3.416	0.231	118	0.205	2078	0.206	2196	0.934	0.936	100	0.193
3.416-3.621	0.23	127	0.206	1947	0.207	2074	0.933	0.94	100	0.196
3.621-3.866	0.207	123	0.174	1848	0.176	1971	0.957	0.964	100	0.17
3.866-4.17	0.159	91	0.144	1733	0.145	1824	0.975	0.972	100	0.144
4.17-4.559	0.181	93	0.137	1624	0.139	1717	0.966	0.974	100	0.14
4.559-5.083	0.169	80	0.144	1449	0.145	1529	0.971	0.971	100	0.15
5.083-5.841	0.235	54	0.174	1303	0.176	1357	0.938	0.96	100	0.18
5.841-7.085	0.222	57	0.178	1124	0.18	1181	0.948	0.963	100	0.185
7.085-9.746	0.134	39	0.142	893	0.142	932	0.975	0.976	100	0.162
9.746-29.705	0.242	26	0.22	556	0.221	582	0.947	0.953	100	0.245

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